

<!--XBRL document created by RR Donnelley Tagger version 10.0.0.218; Copyright (C) RR Donnelley-->
<!--Based on XBRL 2.1-->
<link:linkbase xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://www.xbrl.org/2003/linkbase" xmlns:xbrldt="http://xbrl.org/2005/xbrldt" xmlns:link="http://www.xbrl.org/2003/linkbase" xsi:schemaLocation="http://www.xbrl.org/2003/linkbase http://www.xbrl.org/2003/xbrl-linkbase-2003-12-31.xsd">
  <link:roleRef xlink:type="simple" xlink:href="mnov-20120930.xsd#AvigenTransactionDetailsTexual" roleURI="http://www.medicinova.com/role/AvigenTransactionDetailsTexual" />
  <link:roleRef xlink:type="simple" xlink:href="mnov-20120930.xsd#FairValueMeasurementsDetails" roleURI="http://www.medicinova.com/role/FairValueMeasurementsDetails" />
  <link:roleRef xlink:type="simple" xlink:href="mnov-20120930.xsd#DebtDetails" roleURI="http://www.medicinova.com/role/DebtDetails" />
  <link:roleRef xlink:type="simple" xlink:href="mnov-20120930.xsd#NetLossPerShareDetails" roleURI="http://www.medicinova.com/role/NetLossPerShareDetails" />
  <link:roleRef xlink:type="simple" xlink:href="mnov-20120930.xsd#BalanceSheetDetailDetails" roleURI="http://www.medicinova.com/role/BalanceSheetDetailDetails" />
  <link:roleRef xlink:type="simple" xlink:href="mnov-20120930.xsd#ShareBasedPaymentsDetails" roleURI="http://www.medicinova.com/role/ShareBasedPaymentsDetails" />
  <link:roleRef xlink:type="simple" xlink:href="mnov-20120930.xsd#ShareBasedPaymentsDetailsTextual" roleURI="http://www.medicinova.com/role/ShareBasedPaymentsDetailsTextual" />
  <link:roleRef xlink:type="simple" xlink:href="mnov-20120930.xsd#StockholdersEquityDetailsTextual" roleURI="http://www.medicinova.com/role/StockholdersEquityDetailsTextual" />
  <link:arcroleRef xlink:type="simple" xlink:href="http://www.xbrl.org/2005/xbrldt-2005.xsd#hypercube-dimension" arcroleURI="http://xbrl.org/int/dim/arcrole/hypercube-dimension" />
  <link:arcroleRef xlink:type="simple" xlink:href="http://www.xbrl.org/2005/xbrldt-2005.xsd#dimension-domain" arcroleURI="http://xbrl.org/int/dim/arcrole/dimension-domain" />
  <link:arcroleRef xlink:type="simple" xlink:href="http://www.xbrl.org/2005/xbrldt-2005.xsd#dimension-default" arcroleURI="http://xbrl.org/int/dim/arcrole/dimension-default" />
  <link:arcroleRef xlink:type="simple" xlink:href="http://www.xbrl.org/2005/xbrldt-2005.xsd#domain-member" arcroleURI="http://xbrl.org/int/dim/arcrole/domain-member" />
  <link:arcroleRef xlink:type="simple" xlink:href="http://www.xbrl.org/2005/xbrldt-2005.xsd#all" arcroleURI="http://xbrl.org/int/dim/arcrole/all" />
  <!-- Hypercube Definition (Line Items to Hypercube)-->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/AvigenTransactionDetailsTexual" xlink:title="0602 - Disclosure - Avigen Transaction (Details)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ScheduleOfBusinessAcquisitionsByAcquisitionTable" xlink:label="us-gaap_ScheduleOfBusinessAcquisitionsByAcquisitionTable" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_BusinessAcquisitionAxis" xlink:label="us-gaap_BusinessAcquisitionAxis" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfBusinessAcquisitionsByAcquisitionTable" xlink:to="us-gaap_BusinessAcquisitionAxis" order="1" />
  </link:definitionLink>
  <!-- Domain Members -->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/AvigenTransactionDetailsTexual" xlink:title="0602 - Disclosure - Avigen Transaction (Details)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_BusinessAcquisitionAxis" xlink:label="us-gaap_BusinessAcquisitionAxis" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_BusinessAcquisitionAcquireeDomain" xlink:label="us-gaap_BusinessAcquisitionAcquireeDomain" />
    <link:loc xlink:type="locator" xlink:href="mnov-20120930.xsd#mnov_AvigenMember" xlink:label="mnov_AvigenMember" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_BusinessAcquisitionAxis" xlink:to="us-gaap_BusinessAcquisitionAcquireeDomain" order="1" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_BusinessAcquisitionAcquireeDomain" xlink:to="mnov_AvigenMember" order="1" />
  </link:definitionLink>
  <!-- Hypercube Definition (All)-->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/AvigenTransactionDetailsTexual" xlink:title="0602 - Disclosure - Avigen Transaction (Details)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ScheduleOfBusinessAcquisitionsByAcquisitionTable" xlink:label="us-gaap_ScheduleOfBusinessAcquisitionsByAcquisitionTable" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_BusinessAcquisitionLineItems" xlink:label="us-gaap_BusinessAcquisitionLineItems" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_BusinessAcquisitionLineItems" xlink:to="us-gaap_ScheduleOfBusinessAcquisitionsByAcquisitionTable" order="2" xbrldt:closed="true" xbrldt:contextElement="segment" />
  </link:definitionLink>
  <!-- Inheritance for Line Items:  us-gaap:BusinessAcquisitionLineItems-->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/AvigenTransactionDetailsTexual" xlink:title="0602 - Disclosure - Avigen Transaction (Details)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_BusinessAcquisitionLineItems" xlink:label="us-gaap_BusinessAcquisitionLineItems" />
    <link:loc xlink:type="locator" xlink:href="mnov-20120930.xsd#mnov_BusinessAcquisitionTextualAbstract" xlink:label="mnov_BusinessAcquisitionTextualAbstract" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_BusinessAcquisitionPercentageOfVotingInterestsAcquired" xlink:label="us-gaap_BusinessAcquisitionPercentageOfVotingInterestsAcquired" />
    <link:loc xlink:type="locator" xlink:href="mnov-20120930.xsd#mnov_BusinessAcquisitionCostOfAcquiredEntitySecuredConvertibleNotesIssued" xlink:label="mnov_BusinessAcquisitionCostOfAcquiredEntitySecuredConvertibleNotesIssued" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_DebtInstrumentMaturityDate" xlink:label="us-gaap_DebtInstrumentMaturityDate" />
    <link:loc xlink:type="locator" xlink:href="mnov-20120930.xsd#mnov_BusinessAcquisitionCostOfAcquiredEntitySecuredConvertibleNotesIssuedConversionPricePerShare" xlink:label="mnov_BusinessAcquisitionCostOfAcquiredEntitySecuredConvertibleNotesIssuedConversionPricePerShare" />
    <link:loc xlink:type="locator" xlink:href="mnov-20120930.xsd#mnov_BusinessAcquisitionCostOfAcquiredEntityCashPaidPerShareHeld" xlink:label="mnov_BusinessAcquisitionCostOfAcquiredEntityCashPaidPerShareHeld" />
    <link:loc xlink:type="locator" xlink:href="mnov-20120930.xsd#mnov_BusinessAcquisitionNumberOfConsiderationInstallments" xlink:label="mnov_BusinessAcquisitionNumberOfConsiderationInstallments" />
    <link:loc xlink:type="locator" xlink:href="mnov-20120930.xsd#mnov_BusinessAcquisitionCostOfAcquiredEntityCashPaidInstallmentOne" xlink:label="mnov_BusinessAcquisitionCostOfAcquiredEntityCashPaidInstallmentOne" />
    <link:loc xlink:type="locator" xlink:href="mnov-20120930.xsd#mnov_BusinessAcquisitionCostOfAcquiredEntityCashPaidInstallmentTwo" xlink:label="mnov_BusinessAcquisitionCostOfAcquiredEntityCashPaidInstallmentTwo" />
    <link:loc xlink:type="locator" xlink:href="mnov-20120930.xsd#mnov_BusinessAcquisitionCostOfAcquiredEntityAdditionalConvertibleNotesIssuedInstallmentOne" xlink:label="mnov_BusinessAcquisitionCostOfAcquiredEntityAdditionalConvertibleNotesIssuedInstallmentOne" />
    <link:loc xlink:type="locator" xlink:href="mnov-20120930.xsd#mnov_BusinessAcquisitionCostOfAcquiredEntityAdditionalConvertibleNotesIssuedInstallmentTwo" xlink:label="mnov_BusinessAcquisitionCostOfAcquiredEntityAdditionalConvertibleNotesIssuedInstallmentTwo" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_BusinessAcquisitionLineItems" xlink:to="us-gaap_BusinessAcquisitionPercentageOfVotingInterestsAcquired" order="2" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_BusinessAcquisitionLineItems" xlink:to="mnov_BusinessAcquisitionCostOfAcquiredEntitySecuredConvertibleNotesIssued" order="3" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_BusinessAcquisitionLineItems" xlink:to="us-gaap_DebtInstrumentMaturityDate" order="4" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_BusinessAcquisitionLineItems" xlink:to="mnov_BusinessAcquisitionCostOfAcquiredEntitySecuredConvertibleNotesIssuedConversionPricePerShare" order="5" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_BusinessAcquisitionLineItems" xlink:to="mnov_BusinessAcquisitionCostOfAcquiredEntityCashPaidPerShareHeld" order="6" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_BusinessAcquisitionLineItems" xlink:to="mnov_BusinessAcquisitionNumberOfConsiderationInstallments" order="7" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_BusinessAcquisitionLineItems" xlink:to="mnov_BusinessAcquisitionCostOfAcquiredEntityCashPaidInstallmentOne" order="8" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_BusinessAcquisitionLineItems" xlink:to="mnov_BusinessAcquisitionCostOfAcquiredEntityCashPaidInstallmentTwo" order="9" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_BusinessAcquisitionLineItems" xlink:to="mnov_BusinessAcquisitionCostOfAcquiredEntityAdditionalConvertibleNotesIssuedInstallmentOne" order="10" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_BusinessAcquisitionLineItems" xlink:to="mnov_BusinessAcquisitionCostOfAcquiredEntityAdditionalConvertibleNotesIssuedInstallmentTwo" order="11" />
  </link:definitionLink>
  <!-- Dimension Defaults -->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/AvigenTransactionDetailsTexual" xlink:title="0602 - Disclosure - Avigen Transaction (Details)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_BusinessAcquisitionAxis" xlink:label="us-gaap_BusinessAcquisitionAxis" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_BusinessAcquisitionAcquireeDomain" xlink:label="us-gaap_BusinessAcquisitionAcquireeDomain" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_BusinessAcquisitionAxis" xlink:to="us-gaap_BusinessAcquisitionAcquireeDomain" order="1" />
  </link:definitionLink>
  <!-- Hypercube Definition (Line Items to Hypercube)-->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/FairValueMeasurementsDetails" xlink:title="0604 - Disclosure - Fair Value Measurements (Details)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable" xlink:label="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_FairValueByMeasurementFrequencyAxis" xlink:label="us-gaap_FairValueByMeasurementFrequencyAxis" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable" xlink:to="us-gaap_FairValueByMeasurementFrequencyAxis" order="1" />
  </link:definitionLink>
  <!-- Domain Members -->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/FairValueMeasurementsDetails" xlink:title="0604 - Disclosure - Fair Value Measurements (Details)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_FairValueByMeasurementFrequencyAxis" xlink:label="us-gaap_FairValueByMeasurementFrequencyAxis" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_FairValueMeasurementFrequencyDomain" xlink:label="us-gaap_FairValueMeasurementFrequencyDomain" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_FairValueMeasurementsRecurringMember" xlink:label="us-gaap_FairValueMeasurementsRecurringMember" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_FairValueByMeasurementFrequencyAxis" xlink:to="us-gaap_FairValueMeasurementFrequencyDomain" order="1" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_FairValueMeasurementFrequencyDomain" xlink:to="us-gaap_FairValueMeasurementsRecurringMember" order="1" />
  </link:definitionLink>
  <!-- Hypercube Definition (Line Items to Hypercube)-->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/FairValueMeasurementsDetails" xlink:title="0604 - Disclosure - Fair Value Measurements (Details)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable" xlink:label="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_FairValueByFairValueHierarchyLevelAxis" xlink:label="us-gaap_FairValueByFairValueHierarchyLevelAxis" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable" xlink:to="us-gaap_FairValueByFairValueHierarchyLevelAxis" order="2" />
  </link:definitionLink>
  <!-- Domain Members -->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/FairValueMeasurementsDetails" xlink:title="0604 - Disclosure - Fair Value Measurements (Details)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_FairValueByFairValueHierarchyLevelAxis" xlink:label="us-gaap_FairValueByFairValueHierarchyLevelAxis" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_FairValueMeasurementsFairValueHierarchyDomain" xlink:label="us-gaap_FairValueMeasurementsFairValueHierarchyDomain" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_FairValueInputsLevel1Member" xlink:label="us-gaap_FairValueInputsLevel1Member" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_FairValueInputsLevel2Member" xlink:label="us-gaap_FairValueInputsLevel2Member" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_FairValueInputsLevel3Member" xlink:label="us-gaap_FairValueInputsLevel3Member" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_FairValueByFairValueHierarchyLevelAxis" xlink:to="us-gaap_FairValueMeasurementsFairValueHierarchyDomain" order="1" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_FairValueMeasurementsFairValueHierarchyDomain" xlink:to="us-gaap_FairValueInputsLevel1Member" order="1" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_FairValueMeasurementsFairValueHierarchyDomain" xlink:to="us-gaap_FairValueInputsLevel2Member" order="2" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_FairValueMeasurementsFairValueHierarchyDomain" xlink:to="us-gaap_FairValueInputsLevel3Member" order="3" />
  </link:definitionLink>
  <!-- Hypercube Definition (All)-->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/FairValueMeasurementsDetails" xlink:title="0604 - Disclosure - Fair Value Measurements (Details)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable" xlink:label="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems" xlink:label="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems" xlink:to="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable" order="3" xbrldt:closed="true" xbrldt:contextElement="segment" />
  </link:definitionLink>
  <!-- Inheritance for Line Items:  us-gaap:FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems-->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/FairValueMeasurementsDetails" xlink:title="0604 - Disclosure - Fair Value Measurements (Details)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems" xlink:label="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_CashAndCashEquivalentsFairValueDisclosure" xlink:label="us-gaap_CashAndCashEquivalentsFairValueDisclosure" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems" xlink:to="us-gaap_CashAndCashEquivalentsFairValueDisclosure" order="1" />
  </link:definitionLink>
  <!-- Dimension Defaults -->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/FairValueMeasurementsDetails" xlink:title="0604 - Disclosure - Fair Value Measurements (Details)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_FairValueByMeasurementFrequencyAxis" xlink:label="us-gaap_FairValueByMeasurementFrequencyAxis" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_FairValueMeasurementFrequencyDomain" xlink:label="us-gaap_FairValueMeasurementFrequencyDomain" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_FairValueByMeasurementFrequencyAxis" xlink:to="us-gaap_FairValueMeasurementFrequencyDomain" order="1" />
  </link:definitionLink>
  <!-- Dimension Defaults -->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/FairValueMeasurementsDetails" xlink:title="0604 - Disclosure - Fair Value Measurements (Details)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_FairValueByFairValueHierarchyLevelAxis" xlink:label="us-gaap_FairValueByFairValueHierarchyLevelAxis" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_FairValueMeasurementsFairValueHierarchyDomain" xlink:label="us-gaap_FairValueMeasurementsFairValueHierarchyDomain" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_FairValueByFairValueHierarchyLevelAxis" xlink:to="us-gaap_FairValueMeasurementsFairValueHierarchyDomain" order="2" />
  </link:definitionLink>
  <!-- Hypercube Definition (Line Items to Hypercube)-->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/DebtDetails" xlink:title="0605 - Disclosure - Long-term Debt (Details)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTable" xlink:label="us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTable" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" xlink:label="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTable" xlink:to="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" order="1" />
  </link:definitionLink>
  <!-- Domain Members -->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/DebtDetails" xlink:title="0605 - Disclosure - Long-term Debt (Details)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" xlink:label="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_AntidilutiveSecuritiesNameDomain" xlink:label="us-gaap_AntidilutiveSecuritiesNameDomain" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_WarrantMember" xlink:label="us-gaap_WarrantMember" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" xlink:to="us-gaap_AntidilutiveSecuritiesNameDomain" order="1" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_AntidilutiveSecuritiesNameDomain" xlink:to="us-gaap_WarrantMember" order="1" />
  </link:definitionLink>
  <!-- Hypercube Definition (All)-->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/DebtDetails" xlink:title="0605 - Disclosure - Long-term Debt (Details)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTable" xlink:label="us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTable" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareLineItems" xlink:label="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareLineItems" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareLineItems" xlink:to="us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTable" order="2" xbrldt:closed="true" xbrldt:contextElement="segment" />
  </link:definitionLink>
  <!-- Inheritance for Line Items:  us-gaap:AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareLineItems-->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/DebtDetails" xlink:title="0605 - Disclosure - Long-term Debt (Details)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareLineItems" xlink:label="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareLineItems" />
    <link:loc xlink:type="locator" xlink:href="mnov-20120930.xsd#mnov_LongTermDebtTextualAbstract" xlink:label="mnov_LongTermDebtTextualAbstract" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ClassOfWarrantOrRightNumberOfSecuritiesCalledByWarrantsOrRights" xlink:label="us-gaap_ClassOfWarrantOrRightNumberOfSecuritiesCalledByWarrantsOrRights" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareLineItems" xlink:to="us-gaap_ClassOfWarrantOrRightNumberOfSecuritiesCalledByWarrantsOrRights" order="2" />
  </link:definitionLink>
  <!-- Dimension Defaults -->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/DebtDetails" xlink:title="0605 - Disclosure - Long-term Debt (Details)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" xlink:label="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_AntidilutiveSecuritiesNameDomain" xlink:label="us-gaap_AntidilutiveSecuritiesNameDomain" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" xlink:to="us-gaap_AntidilutiveSecuritiesNameDomain" order="1" />
  </link:definitionLink>
  <!-- Hypercube Definition (Line Items to Hypercube)-->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/NetLossPerShareDetails" xlink:title="0606 - Disclosure - Net Loss Per Share (Details)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTable" xlink:label="us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTable" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" xlink:label="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTable" xlink:to="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" order="1" />
  </link:definitionLink>
  <!-- Domain Members -->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/NetLossPerShareDetails" xlink:title="0606 - Disclosure - Net Loss Per Share (Details)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" xlink:label="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_AntidilutiveSecuritiesNameDomain" xlink:label="us-gaap_AntidilutiveSecuritiesNameDomain" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ConvertiblePreferredStockMember" xlink:label="us-gaap_ConvertiblePreferredStockMember" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_StockOptionsMember" xlink:label="us-gaap_StockOptionsMember" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_WarrantMember" xlink:label="us-gaap_WarrantMember" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" xlink:to="us-gaap_AntidilutiveSecuritiesNameDomain" order="1" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_AntidilutiveSecuritiesNameDomain" xlink:to="us-gaap_ConvertiblePreferredStockMember" order="1" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_AntidilutiveSecuritiesNameDomain" xlink:to="us-gaap_StockOptionsMember" order="2" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_AntidilutiveSecuritiesNameDomain" xlink:to="us-gaap_WarrantMember" order="3" />
  </link:definitionLink>
  <!-- Hypercube Definition (All)-->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/NetLossPerShareDetails" xlink:title="0606 - Disclosure - Net Loss Per Share (Details)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTable" xlink:label="us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTable" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareLineItems" xlink:label="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareLineItems" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareLineItems" xlink:to="us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTable" order="2" xbrldt:closed="true" xbrldt:contextElement="segment" />
  </link:definitionLink>
  <!-- Inheritance for Line Items:  us-gaap:AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareLineItems-->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/NetLossPerShareDetails" xlink:title="0606 - Disclosure - Net Loss Per Share (Details)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareLineItems" xlink:label="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareLineItems" />
    <link:loc xlink:type="locator" xlink:href="mnov-20120930.xsd#mnov_AntidilutiveSecuritiesExcludedFromComputationOfDilutedEarningsPerShareAbstract" xlink:label="mnov_AntidilutiveSecuritiesExcludedFromComputationOfDilutedEarningsPerShareAbstract" />
    <link:loc xlink:type="locator" xlink:href="mnov-20120930.xsd#mnov_AntidilutiveSecuritiesExcludedFromComputationOfDilutedEarningsPerShareAmount" xlink:label="mnov_AntidilutiveSecuritiesExcludedFromComputationOfDilutedEarningsPerShareAmount" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareLineItems" xlink:to="mnov_AntidilutiveSecuritiesExcludedFromComputationOfDilutedEarningsPerShareAmount" order="2" />
  </link:definitionLink>
  <!-- Dimension Defaults -->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/NetLossPerShareDetails" xlink:title="0606 - Disclosure - Net Loss Per Share (Details)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" xlink:label="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_AntidilutiveSecuritiesNameDomain" xlink:label="us-gaap_AntidilutiveSecuritiesNameDomain" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" xlink:to="us-gaap_AntidilutiveSecuritiesNameDomain" order="1" />
  </link:definitionLink>
  <!-- Hypercube Definition (Line Items to Hypercube)-->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/BalanceSheetDetailDetails" xlink:title="0608 - Disclosure - Balance Sheet Detail (Details)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ScheduleOfIncrementalEffectsOnBalanceSheetApplicationOfSFAS158RecognitionProvisionsTable" xlink:label="us-gaap_ScheduleOfIncrementalEffectsOnBalanceSheetApplicationOfSFAS158RecognitionProvisionsTable" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_BalanceSheetLocationAxis" xlink:label="us-gaap_BalanceSheetLocationAxis" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfIncrementalEffectsOnBalanceSheetApplicationOfSFAS158RecognitionProvisionsTable" xlink:to="us-gaap_BalanceSheetLocationAxis" order="1" />
  </link:definitionLink>
  <!-- Domain Members -->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/BalanceSheetDetailDetails" xlink:title="0608 - Disclosure - Balance Sheet Detail (Details)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_BalanceSheetLocationAxis" xlink:label="us-gaap_BalanceSheetLocationAxis" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_BalanceSheetLocationDomain" xlink:label="us-gaap_BalanceSheetLocationDomain" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ResearchAndDevelopmentExpenseMember" xlink:label="us-gaap_ResearchAndDevelopmentExpenseMember" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ProfessionalFeesMember" xlink:label="us-gaap_ProfessionalFeesMember" />
    <link:loc xlink:type="locator" xlink:href="mnov-20120930.xsd#mnov_InvestmentsInAffiliatesSubsidiariesAssociatesAndJointVenturesMember" xlink:label="mnov_InvestmentsInAffiliatesSubsidiariesAssociatesAndJointVenturesMember" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_AccruedLiabilitiesMember" xlink:label="us-gaap_AccruedLiabilitiesMember" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_BalanceSheetLocationAxis" xlink:to="us-gaap_BalanceSheetLocationDomain" order="1" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_BalanceSheetLocationDomain" xlink:to="us-gaap_ResearchAndDevelopmentExpenseMember" order="1" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_BalanceSheetLocationDomain" xlink:to="us-gaap_ProfessionalFeesMember" order="2" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_BalanceSheetLocationDomain" xlink:to="mnov_InvestmentsInAffiliatesSubsidiariesAssociatesAndJointVenturesMember" order="3" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_BalanceSheetLocationDomain" xlink:to="us-gaap_AccruedLiabilitiesMember" order="4" />
  </link:definitionLink>
  <!-- Hypercube Definition (All)-->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/BalanceSheetDetailDetails" xlink:title="0608 - Disclosure - Balance Sheet Detail (Details)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ScheduleOfIncrementalEffectsOnBalanceSheetApplicationOfSFAS158RecognitionProvisionsTable" xlink:label="us-gaap_ScheduleOfIncrementalEffectsOnBalanceSheetApplicationOfSFAS158RecognitionProvisionsTable" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_IncrementalEffectOnBalanceSheetApplicationOfSFAS158RecognitionProvisionsLineItems" xlink:label="us-gaap_IncrementalEffectOnBalanceSheetApplicationOfSFAS158RecognitionProvisionsLineItems" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_IncrementalEffectOnBalanceSheetApplicationOfSFAS158RecognitionProvisionsLineItems" xlink:to="us-gaap_ScheduleOfIncrementalEffectsOnBalanceSheetApplicationOfSFAS158RecognitionProvisionsTable" order="2" xbrldt:closed="true" xbrldt:contextElement="segment" />
  </link:definitionLink>
  <!-- Inheritance for Line Items:  us-gaap:IncrementalEffectOnBalanceSheetApplicationOfSFAS158RecognitionProvisionsLineItems-->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/BalanceSheetDetailDetails" xlink:title="0608 - Disclosure - Balance Sheet Detail (Details)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_IncrementalEffectOnBalanceSheetApplicationOfSFAS158RecognitionProvisionsLineItems" xlink:label="us-gaap_IncrementalEffectOnBalanceSheetApplicationOfSFAS158RecognitionProvisionsLineItems" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_AccruedLiabilitiesCurrentAbstract" xlink:label="us-gaap_AccruedLiabilitiesCurrentAbstract" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_AccruedLiabilitiesCurrent" xlink:label="us-gaap_AccruedLiabilitiesCurrent" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_IncrementalEffectOnBalanceSheetApplicationOfSFAS158RecognitionProvisionsLineItems" xlink:to="us-gaap_AccruedLiabilitiesCurrent" order="2" />
  </link:definitionLink>
  <!-- Dimension Defaults -->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/BalanceSheetDetailDetails" xlink:title="0608 - Disclosure - Balance Sheet Detail (Details)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_BalanceSheetLocationAxis" xlink:label="us-gaap_BalanceSheetLocationAxis" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_BalanceSheetLocationDomain" xlink:label="us-gaap_BalanceSheetLocationDomain" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_BalanceSheetLocationAxis" xlink:to="us-gaap_BalanceSheetLocationDomain" order="1" />
  </link:definitionLink>
  <!-- Hypercube Definition (Line Items to Hypercube)-->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/ShareBasedPaymentsDetails" xlink:title="0609 - Disclosure - Stock-Based Compensation (Details)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:label="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_OptionIndexedToIssuersEquityTypeAxis" xlink:label="us-gaap_OptionIndexedToIssuersEquityTypeAxis" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_OptionIndexedToIssuersEquityTypeAxis" order="1" />
  </link:definitionLink>
  <!-- Domain Members -->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/ShareBasedPaymentsDetails" xlink:title="0609 - Disclosure - Stock-Based Compensation (Details)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_OptionIndexedToIssuersEquityTypeAxis" xlink:label="us-gaap_OptionIndexedToIssuersEquityTypeAxis" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_OptionIndexedToIssuersEquityTypeDomain" xlink:label="us-gaap_OptionIndexedToIssuersEquityTypeDomain" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_EmployeeStockOptionMember" xlink:label="us-gaap_EmployeeStockOptionMember" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_OptionIndexedToIssuersEquityTypeAxis" xlink:to="us-gaap_OptionIndexedToIssuersEquityTypeDomain" order="1" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_OptionIndexedToIssuersEquityTypeDomain" xlink:to="us-gaap_EmployeeStockOptionMember" order="1" />
  </link:definitionLink>
  <!-- Hypercube Definition (Line Items to Hypercube)-->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/ShareBasedPaymentsDetails" xlink:title="0609 - Disclosure - Stock-Based Compensation (Details)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:label="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_MajorTypesOfDebtAndEquitySecuritiesAxis" xlink:label="us-gaap_MajorTypesOfDebtAndEquitySecuritiesAxis" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_MajorTypesOfDebtAndEquitySecuritiesAxis" order="2" />
  </link:definitionLink>
  <!-- Domain Members -->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/ShareBasedPaymentsDetails" xlink:title="0609 - Disclosure - Stock-Based Compensation (Details)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_MajorTypesOfDebtAndEquitySecuritiesAxis" xlink:label="us-gaap_MajorTypesOfDebtAndEquitySecuritiesAxis" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_MajorTypesOfDebtAndEquitySecuritiesDomain" xlink:label="us-gaap_MajorTypesOfDebtAndEquitySecuritiesDomain" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_StockOptionMember" xlink:label="us-gaap_StockOptionMember" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_MajorTypesOfDebtAndEquitySecuritiesAxis" xlink:to="us-gaap_MajorTypesOfDebtAndEquitySecuritiesDomain" order="1" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_MajorTypesOfDebtAndEquitySecuritiesDomain" xlink:to="us-gaap_StockOptionMember" order="1" />
  </link:definitionLink>
  <!-- Hypercube Definition (All)-->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/ShareBasedPaymentsDetails" xlink:title="0609 - Disclosure - Stock-Based Compensation (Details)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:label="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" order="3" xbrldt:closed="true" xbrldt:contextElement="segment" />
  </link:definitionLink>
  <!-- Inheritance for Line Items:  us-gaap:ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems-->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/ShareBasedPaymentsDetails" xlink:title="0609 - Disclosure - Stock-Based Compensation (Details)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsAndMethodologyAbstract" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsAndMethodologyAbstract" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsRiskFreeInterestRate" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsRiskFreeInterestRate" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsExpectedVolatilityRate" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsExpectedVolatilityRate" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsExpectedDividendRate" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsExpectedDividendRate" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardFairValueAssumptionsExpectedTerm1" xlink:label="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardFairValueAssumptionsExpectedTerm1" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsRiskFreeInterestRate" order="2" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsExpectedVolatilityRate" order="3" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsExpectedDividendRate" order="4" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardFairValueAssumptionsExpectedTerm1" order="5" />
  </link:definitionLink>
  <!-- Dimension Defaults -->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/ShareBasedPaymentsDetails" xlink:title="0609 - Disclosure - Stock-Based Compensation (Details)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_OptionIndexedToIssuersEquityTypeAxis" xlink:label="us-gaap_OptionIndexedToIssuersEquityTypeAxis" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_OptionIndexedToIssuersEquityTypeDomain" xlink:label="us-gaap_OptionIndexedToIssuersEquityTypeDomain" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_OptionIndexedToIssuersEquityTypeAxis" xlink:to="us-gaap_OptionIndexedToIssuersEquityTypeDomain" order="1" />
  </link:definitionLink>
  <!-- Dimension Defaults -->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/ShareBasedPaymentsDetails" xlink:title="0609 - Disclosure - Stock-Based Compensation (Details)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_MajorTypesOfDebtAndEquitySecuritiesAxis" xlink:label="us-gaap_MajorTypesOfDebtAndEquitySecuritiesAxis" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_MajorTypesOfDebtAndEquitySecuritiesDomain" xlink:label="us-gaap_MajorTypesOfDebtAndEquitySecuritiesDomain" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_MajorTypesOfDebtAndEquitySecuritiesAxis" xlink:to="us-gaap_MajorTypesOfDebtAndEquitySecuritiesDomain" order="2" />
  </link:definitionLink>
  <!-- Hypercube Definition (Line Items to Hypercube)-->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/ShareBasedPaymentsDetailsTextual" xlink:title="06091 - Disclosure - Stock-Based Compensation (Details Textual)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:label="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_MajorTypesOfDebtAndEquitySecuritiesAxis" xlink:label="us-gaap_MajorTypesOfDebtAndEquitySecuritiesAxis" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_MajorTypesOfDebtAndEquitySecuritiesAxis" order="1" />
  </link:definitionLink>
  <!-- Domain Members -->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/ShareBasedPaymentsDetailsTextual" xlink:title="06091 - Disclosure - Stock-Based Compensation (Details Textual)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_MajorTypesOfDebtAndEquitySecuritiesAxis" xlink:label="us-gaap_MajorTypesOfDebtAndEquitySecuritiesAxis" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_MajorTypesOfDebtAndEquitySecuritiesDomain" xlink:label="us-gaap_MajorTypesOfDebtAndEquitySecuritiesDomain" />
    <link:loc xlink:type="locator" xlink:href="mnov-20120930.xsd#mnov_StockOptionsAndEmployeeStockPurchasePlanMember" xlink:label="mnov_StockOptionsAndEmployeeStockPurchasePlanMember" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_MajorTypesOfDebtAndEquitySecuritiesAxis" xlink:to="us-gaap_MajorTypesOfDebtAndEquitySecuritiesDomain" order="1" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_MajorTypesOfDebtAndEquitySecuritiesDomain" xlink:to="mnov_StockOptionsAndEmployeeStockPurchasePlanMember" order="1" />
  </link:definitionLink>
  <!-- Hypercube Definition (All)-->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/ShareBasedPaymentsDetailsTextual" xlink:title="06091 - Disclosure - Stock-Based Compensation (Details Textual)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:label="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" order="2" xbrldt:closed="true" xbrldt:contextElement="segment" />
  </link:definitionLink>
  <!-- Inheritance for Line Items:  us-gaap:ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems-->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/ShareBasedPaymentsDetailsTextual" xlink:title="06091 - Disclosure - Stock-Based Compensation (Details Textual)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" />
    <link:loc xlink:type="locator" xlink:href="mnov-20120930.xsd#mnov_StockBasedCompensationTextualAbstract" xlink:label="mnov_StockBasedCompensationTextualAbstract" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_AllocatedShareBasedCompensationExpense" xlink:label="us-gaap_AllocatedShareBasedCompensationExpense" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ShareBasedCompensation" xlink:label="us-gaap_ShareBasedCompensation" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ResearchAndDevelopmentExpense" xlink:label="us-gaap_ResearchAndDevelopmentExpense" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_AllocatedShareBasedCompensationExpense" order="2" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensation" order="3" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ResearchAndDevelopmentExpense" order="4" />
  </link:definitionLink>
  <!-- Dimension Defaults -->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/ShareBasedPaymentsDetailsTextual" xlink:title="06091 - Disclosure - Stock-Based Compensation (Details Textual)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_MajorTypesOfDebtAndEquitySecuritiesAxis" xlink:label="us-gaap_MajorTypesOfDebtAndEquitySecuritiesAxis" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_MajorTypesOfDebtAndEquitySecuritiesDomain" xlink:label="us-gaap_MajorTypesOfDebtAndEquitySecuritiesDomain" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_MajorTypesOfDebtAndEquitySecuritiesAxis" xlink:to="us-gaap_MajorTypesOfDebtAndEquitySecuritiesDomain" order="1" />
  </link:definitionLink>
  <!-- Hypercube Definition (Line Items to Hypercube)-->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/StockholdersEquityDetailsTextual" xlink:title="06121 - Disclosure - Stockholders' Equity (Details Textual)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ScheduleOfStockByClassTable" xlink:label="us-gaap_ScheduleOfStockByClassTable" />
    <link:loc xlink:type="locator" xlink:href="mnov-20120930.xsd#mnov_CommonStockPurchaseAgreementPurchaserNameAxis" xlink:label="mnov_CommonStockPurchaseAgreementPurchaserNameAxis" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfStockByClassTable" xlink:to="mnov_CommonStockPurchaseAgreementPurchaserNameAxis" order="1" />
  </link:definitionLink>
  <!-- Domain Members -->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/StockholdersEquityDetailsTextual" xlink:title="06121 - Disclosure - Stockholders' Equity (Details Textual)">
    <link:loc xlink:type="locator" xlink:href="mnov-20120930.xsd#mnov_CommonStockPurchaseAgreementPurchaserNameAxis" xlink:label="mnov_CommonStockPurchaseAgreementPurchaserNameAxis" />
    <link:loc xlink:type="locator" xlink:href="mnov-20120930.xsd#mnov_CommonStockPurchaseAgreementPurchaserNameDomain" xlink:label="mnov_CommonStockPurchaseAgreementPurchaserNameDomain" />
    <link:loc xlink:type="locator" xlink:href="mnov-20120930.xsd#mnov_AspireMember" xlink:label="mnov_AspireMember" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="mnov_CommonStockPurchaseAgreementPurchaserNameAxis" xlink:to="mnov_CommonStockPurchaseAgreementPurchaserNameDomain" order="1" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="mnov_CommonStockPurchaseAgreementPurchaserNameDomain" xlink:to="mnov_AspireMember" order="1" />
  </link:definitionLink>
  <!-- Hypercube Definition (Line Items to Hypercube)-->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/StockholdersEquityDetailsTextual" xlink:title="06121 - Disclosure - Stockholders' Equity (Details Textual)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ScheduleOfStockByClassTable" xlink:label="us-gaap_ScheduleOfStockByClassTable" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.sec.gov/dei/2012/dei-2012-01-31.xsd#dei_LegalEntityAxis" xlink:label="dei_LegalEntityAxis" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfStockByClassTable" xlink:to="dei_LegalEntityAxis" order="2" />
  </link:definitionLink>
  <!-- Domain Members -->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/StockholdersEquityDetailsTextual" xlink:title="06121 - Disclosure - Stockholders' Equity (Details Textual)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.sec.gov/dei/2012/dei-2012-01-31.xsd#dei_LegalEntityAxis" xlink:label="dei_LegalEntityAxis" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.sec.gov/dei/2012/dei-2012-01-31.xsd#dei_EntityDomain" xlink:label="dei_EntityDomain" />
    <link:loc xlink:type="locator" xlink:href="mnov-20120930.xsd#mnov_RedingtonMember" xlink:label="mnov_RedingtonMember" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="dei_LegalEntityAxis" xlink:to="dei_EntityDomain" order="1" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="dei_EntityDomain" xlink:to="mnov_RedingtonMember" order="1" />
  </link:definitionLink>
  <!-- Hypercube Definition (Line Items to Hypercube)-->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/StockholdersEquityDetailsTextual" xlink:title="06121 - Disclosure - Stockholders' Equity (Details Textual)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ScheduleOfStockByClassTable" xlink:label="us-gaap_ScheduleOfStockByClassTable" />
    <link:loc xlink:type="locator" xlink:href="mnov-20120930.xsd#mnov_SharePurchaseAgreementAxis" xlink:label="mnov_SharePurchaseAgreementAxis" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfStockByClassTable" xlink:to="mnov_SharePurchaseAgreementAxis" order="3" />
  </link:definitionLink>
  <!-- Domain Members -->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/StockholdersEquityDetailsTextual" xlink:title="06121 - Disclosure - Stockholders' Equity (Details Textual)">
    <link:loc xlink:type="locator" xlink:href="mnov-20120930.xsd#mnov_SharePurchaseAgreementAxis" xlink:label="mnov_SharePurchaseAgreementAxis" />
    <link:loc xlink:type="locator" xlink:href="mnov-20120930.xsd#mnov_SharePurchaseAgreementDomain" xlink:label="mnov_SharePurchaseAgreementDomain" />
    <link:loc xlink:type="locator" xlink:href="mnov-20120930.xsd#mnov_SharePurchaseAgreementMember" xlink:label="mnov_SharePurchaseAgreementMember" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="mnov_SharePurchaseAgreementAxis" xlink:to="mnov_SharePurchaseAgreementDomain" order="1" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="mnov_SharePurchaseAgreementDomain" xlink:to="mnov_SharePurchaseAgreementMember" order="1" />
  </link:definitionLink>
  <!-- Hypercube Definition (Line Items to Hypercube)-->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/StockholdersEquityDetailsTextual" xlink:title="06121 - Disclosure - Stockholders' Equity (Details Textual)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ScheduleOfStockByClassTable" xlink:label="us-gaap_ScheduleOfStockByClassTable" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_StatementEquityComponentsAxis" xlink:label="us-gaap_StatementEquityComponentsAxis" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfStockByClassTable" xlink:to="us-gaap_StatementEquityComponentsAxis" order="4" />
  </link:definitionLink>
  <!-- Domain Members -->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/StockholdersEquityDetailsTextual" xlink:title="06121 - Disclosure - Stockholders' Equity (Details Textual)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_StatementEquityComponentsAxis" xlink:label="us-gaap_StatementEquityComponentsAxis" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_EquityComponentDomain" xlink:label="us-gaap_EquityComponentDomain" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_CommonStockMember" xlink:label="us-gaap_CommonStockMember" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_StatementEquityComponentsAxis" xlink:to="us-gaap_EquityComponentDomain" order="1" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_EquityComponentDomain" xlink:to="us-gaap_CommonStockMember" order="1" />
  </link:definitionLink>
  <!-- Hypercube Definition (Line Items to Hypercube)-->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/StockholdersEquityDetailsTextual" xlink:title="06121 - Disclosure - Stockholders' Equity (Details Textual)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ScheduleOfStockByClassTable" xlink:label="us-gaap_ScheduleOfStockByClassTable" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_StatementClassOfStockAxis" xlink:label="us-gaap_StatementClassOfStockAxis" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfStockByClassTable" xlink:to="us-gaap_StatementClassOfStockAxis" order="5" />
  </link:definitionLink>
  <!-- Domain Members -->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/StockholdersEquityDetailsTextual" xlink:title="06121 - Disclosure - Stockholders' Equity (Details Textual)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_StatementClassOfStockAxis" xlink:label="us-gaap_StatementClassOfStockAxis" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ClassOfStockDomain" xlink:label="us-gaap_ClassOfStockDomain" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_SeriesBPreferredStockMember" xlink:label="us-gaap_SeriesBPreferredStockMember" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_StatementClassOfStockAxis" xlink:to="us-gaap_ClassOfStockDomain" order="1" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ClassOfStockDomain" xlink:to="us-gaap_SeriesBPreferredStockMember" order="1" />
  </link:definitionLink>
  <!-- Hypercube Definition (Line Items to Hypercube)-->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/StockholdersEquityDetailsTextual" xlink:title="06121 - Disclosure - Stockholders' Equity (Details Textual)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ScheduleOfStockByClassTable" xlink:label="us-gaap_ScheduleOfStockByClassTable" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ShortTermDebtTypeAxis" xlink:label="us-gaap_ShortTermDebtTypeAxis" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfStockByClassTable" xlink:to="us-gaap_ShortTermDebtTypeAxis" order="6" />
  </link:definitionLink>
  <!-- Domain Members -->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/StockholdersEquityDetailsTextual" xlink:title="06121 - Disclosure - Stockholders' Equity (Details Textual)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ShortTermDebtTypeAxis" xlink:label="us-gaap_ShortTermDebtTypeAxis" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ShortTermDebtTypeDomain" xlink:label="us-gaap_ShortTermDebtTypeDomain" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ConvertibleNotesPayableMember" xlink:label="us-gaap_ConvertibleNotesPayableMember" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_ShortTermDebtTypeAxis" xlink:to="us-gaap_ShortTermDebtTypeDomain" order="1" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShortTermDebtTypeDomain" xlink:to="us-gaap_ConvertibleNotesPayableMember" order="1" />
  </link:definitionLink>
  <!-- Hypercube Definition (Line Items to Hypercube)-->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/StockholdersEquityDetailsTextual" xlink:title="06121 - Disclosure - Stockholders' Equity (Details Textual)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ScheduleOfStockByClassTable" xlink:label="us-gaap_ScheduleOfStockByClassTable" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_RangeAxis" xlink:label="us-gaap_RangeAxis" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfStockByClassTable" xlink:to="us-gaap_RangeAxis" order="7" />
  </link:definitionLink>
  <!-- Domain Members -->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/StockholdersEquityDetailsTextual" xlink:title="06121 - Disclosure - Stockholders' Equity (Details Textual)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_RangeAxis" xlink:label="us-gaap_RangeAxis" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_RangeMember" xlink:label="us-gaap_RangeMember" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_MinimumMember" xlink:label="us-gaap_MinimumMember" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_MaximumMember" xlink:label="us-gaap_MaximumMember" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_RangeAxis" xlink:to="us-gaap_RangeMember" order="1" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RangeMember" xlink:to="us-gaap_MinimumMember" order="1" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RangeMember" xlink:to="us-gaap_MaximumMember" order="2" />
  </link:definitionLink>
  <!-- Hypercube Definition (Line Items to Hypercube)-->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/StockholdersEquityDetailsTextual" xlink:title="06121 - Disclosure - Stockholders' Equity (Details Textual)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ScheduleOfStockByClassTable" xlink:label="us-gaap_ScheduleOfStockByClassTable" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ShareholdersEquityClassAxis" xlink:label="us-gaap_ShareholdersEquityClassAxis" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfStockByClassTable" xlink:to="us-gaap_ShareholdersEquityClassAxis" order="8" />
  </link:definitionLink>
  <!-- Domain Members -->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/StockholdersEquityDetailsTextual" xlink:title="06121 - Disclosure - Stockholders' Equity (Details Textual)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ShareholdersEquityClassAxis" xlink:label="us-gaap_ShareholdersEquityClassAxis" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_FairValueByShareholdersEquityClassDomain" xlink:label="us-gaap_FairValueByShareholdersEquityClassDomain" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_WarrantsNotSettleableInCashMember" xlink:label="us-gaap_WarrantsNotSettleableInCashMember" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_ShareholdersEquityClassAxis" xlink:to="us-gaap_FairValueByShareholdersEquityClassDomain" order="1" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_FairValueByShareholdersEquityClassDomain" xlink:to="us-gaap_WarrantsNotSettleableInCashMember" order="1" />
  </link:definitionLink>
  <!-- Hypercube Definition (All)-->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/StockholdersEquityDetailsTextual" xlink:title="06121 - Disclosure - Stockholders' Equity (Details Textual)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ScheduleOfStockByClassTable" xlink:label="us-gaap_ScheduleOfStockByClassTable" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ClassOfStockLineItems" xlink:label="us-gaap_ClassOfStockLineItems" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="us-gaap_ScheduleOfStockByClassTable" order="9" xbrldt:closed="true" xbrldt:contextElement="segment" />
  </link:definitionLink>
  <!-- Inheritance for Line Items:  us-gaap:ClassOfStockLineItems-->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/StockholdersEquityDetailsTextual" xlink:title="06121 - Disclosure - Stockholders' Equity (Details Textual)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ClassOfStockLineItems" xlink:label="us-gaap_ClassOfStockLineItems" />
    <link:loc xlink:type="locator" xlink:href="mnov-20120930.xsd#mnov_StockholdersEquityTextualAbstract" xlink:label="mnov_StockholdersEquityTextualAbstract" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_DebtInstrumentFaceAmount" xlink:label="us-gaap_DebtInstrumentFaceAmount" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_StockIssuedDuringPeriodValueIssuedForCash" xlink:label="us-gaap_StockIssuedDuringPeriodValueIssuedForCash" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_StockIssuedDuringPeriodSharesIssuedForCash" xlink:label="us-gaap_StockIssuedDuringPeriodSharesIssuedForCash" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_CommonStockParOrStatedValuePerShare" xlink:label="us-gaap_CommonStockParOrStatedValuePerShare" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_EquityMethodInvestmentOwnershipPercentage" xlink:label="us-gaap_EquityMethodInvestmentOwnershipPercentage" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_PreferredStockParOrStatedValuePerShare" xlink:label="us-gaap_PreferredStockParOrStatedValuePerShare" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ConvertiblePreferredStockSharesIssuedUponConversion" xlink:label="us-gaap_ConvertiblePreferredStockSharesIssuedUponConversion" />
    <link:loc xlink:type="locator" xlink:href="mnov-20120930.xsd#mnov_MaximumSaleOfCommonStockAuthorizedSharesUnderAgreement" xlink:label="mnov_MaximumSaleOfCommonStockAuthorizedSharesUnderAgreement" />
    <link:loc xlink:type="locator" xlink:href="mnov-20120930.xsd#mnov_ClassOfWarrantsOrRightsExercisePriceOfWarrantsOrRights" xlink:label="mnov_ClassOfWarrantsOrRightsExercisePriceOfWarrantsOrRights" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ClassOfWarrantOrRightNumberOfSecuritiesCalledByWarrantsOrRights" xlink:label="us-gaap_ClassOfWarrantOrRightNumberOfSecuritiesCalledByWarrantsOrRights" />
    <link:loc xlink:type="locator" xlink:href="mnov-20120930.xsd#mnov_MaximumSharesToBePurchasedOnDay" xlink:label="mnov_MaximumSharesToBePurchasedOnDay" />
    <link:loc xlink:type="locator" xlink:href="mnov-20120930.xsd#mnov_MaximumValueOfSharesToBePurchasedOnDay" xlink:label="mnov_MaximumValueOfSharesToBePurchasedOnDay" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_EquityIssuancePerShareAmount" xlink:label="us-gaap_EquityIssuancePerShareAmount" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ProceedsFromIssuanceOfCommonStock" xlink:label="us-gaap_ProceedsFromIssuanceOfCommonStock" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_CommonStockSharesIssued" xlink:label="us-gaap_CommonStockSharesIssued" />
    <link:loc xlink:type="locator" xlink:href="mnov-20120930.xsd#mnov_PercentageOfStockTradedForSharePurchase" xlink:label="mnov_PercentageOfStockTradedForSharePurchase" />
    <link:loc xlink:type="locator" xlink:href="mnov-20120930.xsd#mnov_MaximumExpectedIncreasePercentageOfStockTradedForSharePurchase" xlink:label="mnov_MaximumExpectedIncreasePercentageOfStockTradedForSharePurchase" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_SharePrice" xlink:label="us-gaap_SharePrice" />
    <link:loc xlink:type="locator" xlink:href="mnov-20120930.xsd#mnov_BusinessPercentageForCalculationOfPurchasePrice" xlink:label="mnov_BusinessPercentageForCalculationOfPurchasePrice" />
    <link:loc xlink:type="locator" xlink:href="mnov-20120930.xsd#mnov_ExpiryDurationForWarrants" xlink:label="mnov_ExpiryDurationForWarrants" />
    <link:loc xlink:type="locator" xlink:href="mnov-20120930.xsd#mnov_WarrantFairValue" xlink:label="mnov_WarrantFairValue" />
    <link:loc xlink:type="locator" xlink:href="mnov-20120930.xsd#mnov_DurationForAchievingPriceTargetsForWarrantPricing" xlink:label="mnov_DurationForAchievingPriceTargetsForWarrantPricing" />
    <link:loc xlink:type="locator" xlink:href="mnov-20120930.xsd#mnov_PurchasePriceReferenceNoOfDays" xlink:label="mnov_PurchasePriceReferenceNoOfDays" />
    <link:loc xlink:type="locator" xlink:href="mnov-20120930.xsd#mnov_SaleOfCommonStockExercisePeriodUnderAgreement" xlink:label="mnov_SaleOfCommonStockExercisePeriodUnderAgreement" />
    <link:loc xlink:type="locator" xlink:href="mnov-20120930.xsd#mnov_VolumeOfWeightedAveragePurchaseStock" xlink:label="mnov_VolumeOfWeightedAveragePurchaseStock" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="us-gaap_DebtInstrumentFaceAmount" order="2" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="us-gaap_StockIssuedDuringPeriodValueIssuedForCash" order="3" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="us-gaap_StockIssuedDuringPeriodSharesIssuedForCash" order="4" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="us-gaap_CommonStockParOrStatedValuePerShare" order="5" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="us-gaap_EquityMethodInvestmentOwnershipPercentage" order="6" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="us-gaap_PreferredStockParOrStatedValuePerShare" order="7" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="us-gaap_ConvertiblePreferredStockSharesIssuedUponConversion" order="8" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="mnov_MaximumSaleOfCommonStockAuthorizedSharesUnderAgreement" order="9" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="mnov_ClassOfWarrantsOrRightsExercisePriceOfWarrantsOrRights" order="10" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="us-gaap_ClassOfWarrantOrRightNumberOfSecuritiesCalledByWarrantsOrRights" order="11" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="mnov_MaximumSharesToBePurchasedOnDay" order="12" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="mnov_MaximumValueOfSharesToBePurchasedOnDay" order="13" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="us-gaap_EquityIssuancePerShareAmount" order="14" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="us-gaap_ProceedsFromIssuanceOfCommonStock" order="15" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="us-gaap_CommonStockSharesIssued" order="16" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="mnov_PercentageOfStockTradedForSharePurchase" order="17" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="mnov_MaximumExpectedIncreasePercentageOfStockTradedForSharePurchase" order="18" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="us-gaap_SharePrice" order="19" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="mnov_BusinessPercentageForCalculationOfPurchasePrice" order="20" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="mnov_ExpiryDurationForWarrants" order="21" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="mnov_WarrantFairValue" order="22" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="mnov_DurationForAchievingPriceTargetsForWarrantPricing" order="23" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="mnov_PurchasePriceReferenceNoOfDays" order="24" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="mnov_SaleOfCommonStockExercisePeriodUnderAgreement" order="25" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="mnov_VolumeOfWeightedAveragePurchaseStock" order="26" />
  </link:definitionLink>
  <!-- Dimension Defaults -->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/StockholdersEquityDetailsTextual" xlink:title="06121 - Disclosure - Stockholders' Equity (Details Textual)">
    <link:loc xlink:type="locator" xlink:href="mnov-20120930.xsd#mnov_CommonStockPurchaseAgreementPurchaserNameAxis" xlink:label="mnov_CommonStockPurchaseAgreementPurchaserNameAxis" />
    <link:loc xlink:type="locator" xlink:href="mnov-20120930.xsd#mnov_CommonStockPurchaseAgreementPurchaserNameDomain" xlink:label="mnov_CommonStockPurchaseAgreementPurchaserNameDomain" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="mnov_CommonStockPurchaseAgreementPurchaserNameAxis" xlink:to="mnov_CommonStockPurchaseAgreementPurchaserNameDomain" order="1" />
  </link:definitionLink>
  <!-- Dimension Defaults -->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/StockholdersEquityDetailsTextual" xlink:title="06121 - Disclosure - Stockholders' Equity (Details Textual)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.sec.gov/dei/2012/dei-2012-01-31.xsd#dei_LegalEntityAxis" xlink:label="dei_LegalEntityAxis" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.sec.gov/dei/2012/dei-2012-01-31.xsd#dei_EntityDomain" xlink:label="dei_EntityDomain" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="dei_LegalEntityAxis" xlink:to="dei_EntityDomain" order="2" />
  </link:definitionLink>
  <!-- Dimension Defaults -->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/StockholdersEquityDetailsTextual" xlink:title="06121 - Disclosure - Stockholders' Equity (Details Textual)">
    <link:loc xlink:type="locator" xlink:href="mnov-20120930.xsd#mnov_SharePurchaseAgreementAxis" xlink:label="mnov_SharePurchaseAgreementAxis" />
    <link:loc xlink:type="locator" xlink:href="mnov-20120930.xsd#mnov_SharePurchaseAgreementDomain" xlink:label="mnov_SharePurchaseAgreementDomain" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="mnov_SharePurchaseAgreementAxis" xlink:to="mnov_SharePurchaseAgreementDomain" order="3" />
  </link:definitionLink>
  <!-- Dimension Defaults -->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/StockholdersEquityDetailsTextual" xlink:title="06121 - Disclosure - Stockholders' Equity (Details Textual)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_StatementEquityComponentsAxis" xlink:label="us-gaap_StatementEquityComponentsAxis" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_EquityComponentDomain" xlink:label="us-gaap_EquityComponentDomain" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_StatementEquityComponentsAxis" xlink:to="us-gaap_EquityComponentDomain" order="4" />
  </link:definitionLink>
  <!-- Dimension Defaults -->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/StockholdersEquityDetailsTextual" xlink:title="06121 - Disclosure - Stockholders' Equity (Details Textual)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_StatementClassOfStockAxis" xlink:label="us-gaap_StatementClassOfStockAxis" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ClassOfStockDomain" xlink:label="us-gaap_ClassOfStockDomain" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_StatementClassOfStockAxis" xlink:to="us-gaap_ClassOfStockDomain" order="5" />
  </link:definitionLink>
  <!-- Dimension Defaults -->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/StockholdersEquityDetailsTextual" xlink:title="06121 - Disclosure - Stockholders' Equity (Details Textual)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ShortTermDebtTypeAxis" xlink:label="us-gaap_ShortTermDebtTypeAxis" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ShortTermDebtTypeDomain" xlink:label="us-gaap_ShortTermDebtTypeDomain" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_ShortTermDebtTypeAxis" xlink:to="us-gaap_ShortTermDebtTypeDomain" order="6" />
  </link:definitionLink>
  <!-- Dimension Defaults -->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/StockholdersEquityDetailsTextual" xlink:title="06121 - Disclosure - Stockholders' Equity (Details Textual)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_RangeAxis" xlink:label="us-gaap_RangeAxis" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_RangeMember" xlink:label="us-gaap_RangeMember" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_RangeAxis" xlink:to="us-gaap_RangeMember" order="7" />
  </link:definitionLink>
  <!-- Dimension Defaults -->
  <link:definitionLink xlink:type="extended" xlink:role="http://www.medicinova.com/role/StockholdersEquityDetailsTextual" xlink:title="06121 - Disclosure - Stockholders' Equity (Details Textual)">
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_ShareholdersEquityClassAxis" xlink:label="us-gaap_ShareholdersEquityClassAxis" />
    <link:loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2012/elts/us-gaap-2012-01-31.xsd#us-gaap_FairValueByShareholdersEquityClassDomain" xlink:label="us-gaap_FairValueByShareholdersEquityClassDomain" />
    <link:definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_ShareholdersEquityClassAxis" xlink:to="us-gaap_FairValueByShareholdersEquityClassDomain" order="8" />
  </link:definitionLink>
</link:linkbase>