<?xml version="1.0" encoding="us-ascii"?>
<!--XBRL document created with Crossfire by Rivet Software version 4.3.94.0 http://www.rivetsoftware.com-->
<!--Based on XBRL 2.1-->
<!--Created on: 12/20/2011 1:42:41 PM-->
<!--Modified on: 12/20/2011 1:42:42 PM-->
<linkbase xmlns="http://www.xbrl.org/2003/linkbase" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xbrldt="http://xbrl.org/2005/xbrldt" xsi:schemaLocation="http://www.xbrl.org/2003/linkbase http://www.xbrl.org/2003/xbrl-linkbase-2003-12-31.xsd">
  <roleRef xlink:type="simple" xlink:href="arwr-20110930.xsd#StatementConsolidatedStatementOfStockholdersEquity" roleURI="http://www.arrowheadresearch.com/2010-06-30/role/StatementConsolidatedStatementOfStockholdersEquity" />
  <roleRef xlink:type="simple" xlink:href="arwr-20110930.xsd#StatementConsolidatedStatementOfStockholdersEquityParenthetical" roleURI="http://www.arrowheadresearch.com/2010-06-30/role/StatementConsolidatedStatementOfStockholdersEquityParenthetical" />
  <roleRef xlink:type="simple" xlink:href="arwr-20110930.xsd#StatementConsolidatedStatementsOfCashFlowsParenthetical" roleURI="http://www.arrowheadresearch.com/2010-06-30/role/StatementConsolidatedStatementsOfCashFlowsParenthetical" />
  <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" />
  <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" />
  <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" />
  <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" />
  <arcroleRef xlink:type="simple" xlink:href="http://www.xbrl.org/2005/xbrldt-2005.xsd#all" arcroleURI="http://xbrl.org/int/dim/arcrole/all" />
  <definitionLink xlink:role="http://www.arrowheadresearch.com/2010-06-30/role/StatementConsolidatedStatementOfStockholdersEquity" xlink:type="extended" xlink:title="00300 - Statement - Consolidated Statement Of Stockholders' Equity">
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2011/elts/us-gaap-2011-01-31.xsd#us-gaap_StatementTable" xlink:label="us-gaap_StatementTable" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_CommonStockIssuanceByTypeAxis" xlink:label="arwr_CommonStockIssuanceByTypeAxis" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" order="1" xlink:from="us-gaap_StatementTable" xlink:to="arwr_CommonStockIssuanceByTypeAxis" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_CommonStockIssuanceTypeDomain" xlink:label="arwr_CommonStockIssuanceTypeDomain" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" order="1" xlink:from="arwr_CommonStockIssuanceByTypeAxis" xlink:to="arwr_CommonStockIssuanceTypeDomain" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_CommonStockIssuanceTypeDomain" xlink:label="arwr_CommonStockIssuanceTypeDomain_634599853593449409" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" order="1" xlink:from="arwr_CommonStockIssuanceByTypeAxis" xlink:to="arwr_CommonStockIssuanceTypeDomain_634599853593449409" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedForCashAtZeroPointZeroOneDollarsPerUnitMember" xlink:label="arwr_IssuedForCashAtZeroPointZeroOneDollarsPerUnitMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="1" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedForCashAtZeroPointZeroOneDollarsPerUnitMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedForCashAtTenDollarPerUnitMember" xlink:label="arwr_IssuedForCashAtTenDollarPerUnitMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="2" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedForCashAtTenDollarPerUnitMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedForMarketableSecuritiesAtTenDollarPerUnitMember" xlink:label="arwr_IssuedForMarketableSecuritiesAtTenDollarPerUnitMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="3" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedForMarketableSecuritiesAtTenDollarPerUnitMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedForCashAtFifteenDollarPerUnitMember" xlink:label="arwr_IssuedForCashAtFifteenDollarPerUnitMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="4" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedForCashAtFifteenDollarPerUnitMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_StockIssuanceCostChargedToAdditionalPaidInCapitalMember" xlink:label="arwr_StockIssuanceCostChargedToAdditionalPaidInCapitalMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="5" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_StockIssuanceCostChargedToAdditionalPaidInCapitalMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_ArrowheadsIncreaseInProportionateShareOfInsertTherapeuticsEquityMember" xlink:label="arwr_ArrowheadsIncreaseInProportionateShareOfInsertTherapeuticsEquityMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="6" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_ArrowheadsIncreaseInProportionateShareOfInsertTherapeuticsEquityMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_ArrowheadsIncreaseInProportionateShareOfCalandosEquityMember" xlink:label="arwr_ArrowheadsIncreaseInProportionateShareOfCalandosEquityMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="7" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_ArrowheadsIncreaseInProportionateShareOfCalandosEquityMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedAsGiftForTenDollarAndNinetyCentsPerShareMember" xlink:label="arwr_IssuedAsGiftForTenDollarAndNinetyCentsPerShareMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="8" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedAsGiftForTenDollarAndNinetyCentsPerShareMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedAsStockIssuanceCostAtFifteenDollarPerUnitMember" xlink:label="arwr_IssuedAsStockIssuanceCostAtFifteenDollarPerUnitMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="9" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedAsStockIssuanceCostAtFifteenDollarPerUnitMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_ExercisedAtTwoDollarPerShareMember" xlink:label="arwr_ExercisedAtTwoDollarPerShareMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="10" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_ExercisedAtTwoDollarPerShareMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_ExercisedAtTenDollarPerShareMember" xlink:label="arwr_ExercisedAtTenDollarPerShareMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="11" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_ExercisedAtTenDollarPerShareMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_ExercisedAtFifteenDollarPerShareMember" xlink:label="arwr_ExercisedAtFifteenDollarPerShareMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="12" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_ExercisedAtFifteenDollarPerShareMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedToPurchaseInsertTherapeuticsShareAtThirtyNineDollarsAndEightyCentsPerShareMember" xlink:label="arwr_IssuedToPurchaseInsertTherapeuticsShareAtThirtyNineDollarsAndEightyCentsPerShareMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="13" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedToPurchaseInsertTherapeuticsShareAtThirtyNineDollarsAndEightyCentsPerShareMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedAtFortyEightDollarsAndEightyCentsPerShareMember" xlink:label="arwr_IssuedAtFortyEightDollarsAndEightyCentsPerShareMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="14" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedAtFortyEightDollarsAndEightyCentsPerShareMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedAtThirtyEightDollarsAndFortyCentsPerShareMember" xlink:label="arwr_IssuedAtThirtyEightDollarsAndFortyCentsPerShareMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="15" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedAtThirtyEightDollarsAndFortyCentsPerShareMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedAtThirtyFiveDollarsPerShareMember" xlink:label="arwr_IssuedAtThirtyFiveDollarsPerShareMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="16" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedAtThirtyFiveDollarsPerShareMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedAtFiftyNineDollarsAndTenCentsPerShareMember" xlink:label="arwr_IssuedAtFiftyNineDollarsAndTenCentsPerShareMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="17" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedAtFiftyNineDollarsAndTenCentsPerShareMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedToPurchaseCalandoPharmaceuticalsIncAtFiftyOneDollarsAndSeventyCentsPerShareMember" xlink:label="arwr_IssuedToPurchaseCalandoPharmaceuticalsIncAtFiftyOneDollarsAndSeventyCentsPerShareMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="18" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedToPurchaseCalandoPharmaceuticalsIncAtFiftyOneDollarsAndSeventyCentsPerShareMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedAtFiftySevenDollarsAndEightyCentsPerShareMember" xlink:label="arwr_IssuedAtFiftySevenDollarsAndEightyCentsPerShareMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="19" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedAtFiftySevenDollarsAndEightyCentsPerShareMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedForPurchaseOfCarbonNanotechnologiesIncAtThirtySevenDollarsAndSeventyCentsPerShareMember" xlink:label="arwr_IssuedForPurchaseOfCarbonNanotechnologiesIncAtThirtySevenDollarsAndSeventyCentsPerShareMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="20" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedForPurchaseOfCarbonNanotechnologiesIncAtThirtySevenDollarsAndSeventyCentsPerShareMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedAtApproximatelyEighteenDollarPerShareNetMember" xlink:label="arwr_IssuedAtApproximatelyEighteenDollarPerShareNetMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="21" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedAtApproximatelyEighteenDollarPerShareNetMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedAtTwentySevenDollarsAndTwentyCentsPerShareToRiceUniversityMember" xlink:label="arwr_IssuedAtTwentySevenDollarsAndTwentyCentsPerShareToRiceUniversityMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="22" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedAtTwentySevenDollarsAndTwentyCentsPerShareToRiceUniversityMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedAtTwentyEightDollarsAndThirtyCentsPerShareToPurchaseSharesOfUnidymIncMember" xlink:label="arwr_IssuedAtTwentyEightDollarsAndThirtyCentsPerShareToPurchaseSharesOfUnidymIncMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="23" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedAtTwentyEightDollarsAndThirtyCentsPerShareToPurchaseSharesOfUnidymIncMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedAtTwentyNineDollarsAndFiftyCentsPerShareToPurchaseMasaEnergyLlcMember" xlink:label="arwr_IssuedAtTwentyNineDollarsAndFiftyCentsPerShareToPurchaseMasaEnergyLlcMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="24" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedAtTwentyNineDollarsAndFiftyCentsPerShareToPurchaseMasaEnergyLlcMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedAtTwentyOneDollarsAndNinetyCentsPerShareToUnidymForAcquisitionOfNanoconductionMember" xlink:label="arwr_IssuedAtTwentyOneDollarsAndNinetyCentsPerShareToUnidymForAcquisitionOfNanoconductionMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="25" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedAtTwentyOneDollarsAndNinetyCentsPerShareToUnidymForAcquisitionOfNanoconductionMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedAtTwentyOneDollarsAndEightyCentsPerShareMember" xlink:label="arwr_IssuedAtTwentyOneDollarsAndEightyCentsPerShareMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="26" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedAtTwentyOneDollarsAndEightyCentsPerShareMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedAtFiveDollarsAndFiftyCentsPerShareToUnidymStockholderInExchangeForUnidymSSharesMember" xlink:label="arwr_IssuedAtFiveDollarsAndFiftyCentsPerShareToUnidymStockholderInExchangeForUnidymSSharesMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="27" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedAtFiveDollarsAndFiftyCentsPerShareToUnidymStockholderInExchangeForUnidymSSharesMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedAtFiveDollarsAndTwentyCentsPerShareToTelVenturesInExchangeForUnidymSSharesMember" xlink:label="arwr_IssuedAtFiveDollarsAndTwentyCentsPerShareToTelVenturesInExchangeForUnidymSSharesMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="28" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedAtFiveDollarsAndTwentyCentsPerShareToTelVenturesInExchangeForUnidymSSharesMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedAtThreeDollarsPerShareMember" xlink:label="arwr_IssuedAtThreeDollarsPerShareMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="29" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedAtThreeDollarsPerShareMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedAtSixDollarsAndThirtyCentsPerShareMember" xlink:label="arwr_IssuedAtSixDollarsAndThirtyCentsPerShareMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="30" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedAtSixDollarsAndThirtyCentsPerShareMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedAtThirteenDollarsAndTwelveCentsPerShareMember" xlink:label="arwr_IssuedAtThirteenDollarsAndTwelveCentsPerShareMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="31" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedAtThirteenDollarsAndTwelveCentsPerShareMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedAtThreeDollarsAndEightyCentsPerShareMember" xlink:label="arwr_IssuedAtThreeDollarsAndEightyCentsPerShareMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="32" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedAtThreeDollarsAndEightyCentsPerShareMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuanceOfCommonStockForSubscriptionMember" xlink:label="arwr_IssuanceOfCommonStockForSubscriptionMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="33" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuanceOfCommonStockForSubscriptionMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_SeriesDPreferredStockIssuedForSubscriptionInUnidymMember" xlink:label="arwr_SeriesDPreferredStockIssuedForSubscriptionInUnidymMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="34" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_SeriesDPreferredStockIssuedForSubscriptionInUnidymMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedToUnidymStockholdersInExchangeForUnidymsSharesMember" xlink:label="arwr_IssuedToUnidymStockholdersInExchangeForUnidymsSharesMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="35" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedToUnidymStockholdersInExchangeForUnidymsSharesMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedToCalandoStockholdersInExchangeForCalandoSSharesMember" xlink:label="arwr_IssuedToCalandoStockholdersInExchangeForCalandoSSharesMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="36" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedToCalandoStockholdersInExchangeForCalandoSSharesMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2011/elts/us-gaap-2011-01-31.xsd#us-gaap_StatementEquityComponentsAxis" xlink:label="us-gaap_StatementEquityComponentsAxis" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" order="2" xlink:from="us-gaap_StatementTable" xlink:to="us-gaap_StatementEquityComponentsAxis" use="optional" />
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2011/elts/us-gaap-2011-01-31.xsd#us-gaap_EquityComponentDomain" xlink:label="us-gaap_EquityComponentDomain" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" order="1" xlink:from="us-gaap_StatementEquityComponentsAxis" xlink:to="us-gaap_EquityComponentDomain" use="optional" />
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2011/elts/us-gaap-2011-01-31.xsd#us-gaap_EquityComponentDomain" xlink:label="us-gaap_EquityComponentDomain_634599853593519409" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" order="1" xlink:from="us-gaap_StatementEquityComponentsAxis" xlink:to="us-gaap_EquityComponentDomain_634599853593519409" use="optional" />
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2011/elts/us-gaap-2011-01-31.xsd#us-gaap_ParentMember" xlink:label="us-gaap_ParentMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="1" xlink:from="us-gaap_EquityComponentDomain" xlink:to="us-gaap_ParentMember" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_SubscriptionsReceivableMember" xlink:label="arwr_SubscriptionsReceivableMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="1" xlink:from="us-gaap_ParentMember" xlink:to="arwr_SubscriptionsReceivableMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2011/elts/us-gaap-2011-01-31.xsd#us-gaap_CommonStockMember" xlink:label="us-gaap_CommonStockMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="2" xlink:from="us-gaap_ParentMember" xlink:to="us-gaap_CommonStockMember" use="optional" />
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2011/elts/us-gaap-2011-01-31.xsd#us-gaap_AdditionalPaidInCapitalMember" xlink:label="us-gaap_AdditionalPaidInCapitalMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="3" xlink:from="us-gaap_ParentMember" xlink:to="us-gaap_AdditionalPaidInCapitalMember" use="optional" />
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2011/elts/us-gaap-2011-01-31.xsd#us-gaap_RetainedEarningsMember" xlink:label="us-gaap_RetainedEarningsMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="4" xlink:from="us-gaap_ParentMember" xlink:to="us-gaap_RetainedEarningsMember" use="optional" />
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2011/elts/us-gaap-2011-01-31.xsd#us-gaap_NoncontrollingInterestMember" xlink:label="us-gaap_NoncontrollingInterestMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="2" xlink:from="us-gaap_EquityComponentDomain" xlink:to="us-gaap_NoncontrollingInterestMember" use="optional" />
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2011/elts/us-gaap-2011-01-31.xsd#us-gaap_StatementLineItems" xlink:label="us-gaap_StatementLineItems" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" order="1" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_StatementTable" use="optional" xbrldt:contextElement="segment" xbrldt:closed="true" />
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2011/elts/us-gaap-2011-01-31.xsd#us-gaap_StockIssuedDuringPeriodValueNewIssues" xlink:label="us-gaap_StockIssuedDuringPeriodValueNewIssues" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="2" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_StockIssuedDuringPeriodValueNewIssues" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2011/elts/us-gaap-2011-01-31.xsd#us-gaap_StockIssuedDuringPeriodSharesNewIssues" xlink:label="us-gaap_StockIssuedDuringPeriodSharesNewIssues" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="3" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_StockIssuedDuringPeriodSharesNewIssues" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2011/elts/us-gaap-2011-01-31.xsd#us-gaap_AdjustmentsToAdditionalPaidInCapitalEquityComponentOfConvertibleDebt" xlink:label="us-gaap_AdjustmentsToAdditionalPaidInCapitalEquityComponentOfConvertibleDebt" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="4" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_AdjustmentsToAdditionalPaidInCapitalEquityComponentOfConvertibleDebt" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2011/elts/us-gaap-2011-01-31.xsd#us-gaap_AdjustmentsToAdditionalPaidInCapitalStockIssuedIssuanceCosts" xlink:label="us-gaap_AdjustmentsToAdditionalPaidInCapitalStockIssuedIssuanceCosts" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="5" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_AdjustmentsToAdditionalPaidInCapitalStockIssuedIssuanceCosts" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2011/elts/us-gaap-2011-01-31.xsd#us-gaap_ProfitLoss" xlink:label="us-gaap_ProfitLoss" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="6" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_ProfitLoss" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2011/elts/us-gaap-2011-01-31.xsd#us-gaap_StockIssuedDuringPeriodValueStockOptionsExercised" xlink:label="us-gaap_StockIssuedDuringPeriodValueStockOptionsExercised" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="7" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_StockIssuedDuringPeriodValueStockOptionsExercised" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2011/elts/us-gaap-2011-01-31.xsd#us-gaap_StockIssuedDuringPeriodSharesStockOptionsExercised" xlink:label="us-gaap_StockIssuedDuringPeriodSharesStockOptionsExercised" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="8" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_StockIssuedDuringPeriodSharesStockOptionsExercised" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2011/elts/us-gaap-2011-01-31.xsd#us-gaap_AdjustmentsToAdditionalPaidInCapitalSharebasedCompensationRequisiteServicePeriodRecognitionValue" xlink:label="us-gaap_AdjustmentsToAdditionalPaidInCapitalSharebasedCompensationRequisiteServicePeriodRecognitionValue" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="9" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_AdjustmentsToAdditionalPaidInCapitalSharebasedCompensationRequisiteServicePeriodRecognitionValue" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2011/elts/us-gaap-2011-01-31.xsd#us-gaap_AdjustmentsToAdditionalPaidInCapitalReallocationOfMinorityInterest" xlink:label="us-gaap_AdjustmentsToAdditionalPaidInCapitalReallocationOfMinorityInterest" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="10" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_AdjustmentsToAdditionalPaidInCapitalReallocationOfMinorityInterest" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2011/elts/us-gaap-2011-01-31.xsd#us-gaap_ProceedsFromIssuanceOfPreferredStockAndPreferenceStock" xlink:label="us-gaap_ProceedsFromIssuanceOfPreferredStockAndPreferenceStock" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="11" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_ProceedsFromIssuanceOfPreferredStockAndPreferenceStock" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2011/elts/us-gaap-2011-01-31.xsd#us-gaap_AdjustmentsToAdditionalPaidInCapitalConvertibleDebtWithConversionFeature" xlink:label="us-gaap_AdjustmentsToAdditionalPaidInCapitalConvertibleDebtWithConversionFeature" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="12" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_AdjustmentsToAdditionalPaidInCapitalConvertibleDebtWithConversionFeature" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2011/elts/us-gaap-2011-01-31.xsd#us-gaap_StockholdersEquityIncludingPortionAttributableToNoncontrollingInterest" xlink:label="us-gaap_StockholdersEquityIncludingPortionAttributableToNoncontrollingInterest" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="13" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_StockholdersEquityIncludingPortionAttributableToNoncontrollingInterest" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2011/elts/us-gaap-2011-01-31.xsd#us-gaap_SharesIssued" xlink:label="us-gaap_SharesIssued" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="14" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_SharesIssued" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2011/elts/us-gaap-2011-01-31.xsd#us-gaap_MinorityInterestIncreaseFromStockIssuance" xlink:label="us-gaap_MinorityInterestIncreaseFromStockIssuance" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="15" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_MinorityInterestIncreaseFromStockIssuance" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2011/elts/us-gaap-2011-01-31.xsd#us-gaap_NetIncomeLoss" xlink:label="us-gaap_NetIncomeLoss" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="16" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_NetIncomeLoss" priority="1" use="optional" />
  </definitionLink>
  <definitionLink xlink:role="http://www.arrowheadresearch.com/2010-06-30/role/StatementConsolidatedStatementOfStockholdersEquityParenthetical" xlink:type="extended" xlink:title="00305 - Statement - Consolidated Statement Of Stockholders' Equity (Parenthetical)">
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2011/elts/us-gaap-2011-01-31.xsd#us-gaap_StatementTable" xlink:label="us-gaap_StatementTable" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_CommonStockIssuanceByTypeAxis" xlink:label="arwr_CommonStockIssuanceByTypeAxis" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" order="1" xlink:from="us-gaap_StatementTable" xlink:to="arwr_CommonStockIssuanceByTypeAxis" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_CommonStockIssuanceTypeDomain" xlink:label="arwr_CommonStockIssuanceTypeDomain" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" order="1" xlink:from="arwr_CommonStockIssuanceByTypeAxis" xlink:to="arwr_CommonStockIssuanceTypeDomain" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedForCashAtZeroPointZeroOneDollarsPerUnitMember" xlink:label="arwr_IssuedForCashAtZeroPointZeroOneDollarsPerUnitMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="1" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedForCashAtZeroPointZeroOneDollarsPerUnitMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedForCashAtTenDollarPerUnitMember" xlink:label="arwr_IssuedForCashAtTenDollarPerUnitMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="2" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedForCashAtTenDollarPerUnitMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedForMarketableSecuritiesAtTenDollarPerUnitMember" xlink:label="arwr_IssuedForMarketableSecuritiesAtTenDollarPerUnitMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="3" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedForMarketableSecuritiesAtTenDollarPerUnitMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedForCashAtFifteenDollarPerUnitMember" xlink:label="arwr_IssuedForCashAtFifteenDollarPerUnitMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="4" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedForCashAtFifteenDollarPerUnitMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedAsGiftForTenDollarAndNinetyCentsPerShareMember" xlink:label="arwr_IssuedAsGiftForTenDollarAndNinetyCentsPerShareMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="5" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedAsGiftForTenDollarAndNinetyCentsPerShareMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedAsStockIssuanceCostAtFifteenDollarPerUnitMember" xlink:label="arwr_IssuedAsStockIssuanceCostAtFifteenDollarPerUnitMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="6" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedAsStockIssuanceCostAtFifteenDollarPerUnitMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_ExercisedAtTwoDollarPerShareMember" xlink:label="arwr_ExercisedAtTwoDollarPerShareMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="7" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_ExercisedAtTwoDollarPerShareMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_ExercisedAtTenDollarPerShareMember" xlink:label="arwr_ExercisedAtTenDollarPerShareMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="8" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_ExercisedAtTenDollarPerShareMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_ExercisedAtFifteenDollarPerShareMember" xlink:label="arwr_ExercisedAtFifteenDollarPerShareMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="9" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_ExercisedAtFifteenDollarPerShareMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedAtFortyEightDollarsAndEightyCentsPerShareMember" xlink:label="arwr_IssuedAtFortyEightDollarsAndEightyCentsPerShareMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="10" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedAtFortyEightDollarsAndEightyCentsPerShareMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedToPurchaseInsertTherapeuticsShareAtThirtyNineDollarsAndEightyCentsPerShareMember" xlink:label="arwr_IssuedToPurchaseInsertTherapeuticsShareAtThirtyNineDollarsAndEightyCentsPerShareMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="11" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedToPurchaseInsertTherapeuticsShareAtThirtyNineDollarsAndEightyCentsPerShareMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedAtThirtyEightDollarsAndFortyCentsPerShareMember" xlink:label="arwr_IssuedAtThirtyEightDollarsAndFortyCentsPerShareMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="12" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedAtThirtyEightDollarsAndFortyCentsPerShareMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedAtThirtyFiveDollarsPerShareMember" xlink:label="arwr_IssuedAtThirtyFiveDollarsPerShareMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="13" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedAtThirtyFiveDollarsPerShareMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedAtFiftyNineDollarsAndTenCentsPerShareMember" xlink:label="arwr_IssuedAtFiftyNineDollarsAndTenCentsPerShareMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="14" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedAtFiftyNineDollarsAndTenCentsPerShareMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedToPurchaseCalandoPharmaceuticalsIncAtFiftyOneDollarsAndSeventyCentsPerShareMember" xlink:label="arwr_IssuedToPurchaseCalandoPharmaceuticalsIncAtFiftyOneDollarsAndSeventyCentsPerShareMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="15" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedToPurchaseCalandoPharmaceuticalsIncAtFiftyOneDollarsAndSeventyCentsPerShareMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedAtFiftySevenDollarsAndEightyCentsPerShareMember" xlink:label="arwr_IssuedAtFiftySevenDollarsAndEightyCentsPerShareMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="16" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedAtFiftySevenDollarsAndEightyCentsPerShareMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedForPurchaseOfCarbonNanotechnologiesIncAtThirtySevenDollarsAndSeventyCentsPerShareMember" xlink:label="arwr_IssuedForPurchaseOfCarbonNanotechnologiesIncAtThirtySevenDollarsAndSeventyCentsPerShareMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="17" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedForPurchaseOfCarbonNanotechnologiesIncAtThirtySevenDollarsAndSeventyCentsPerShareMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedAtApproximatelyEighteenDollarPerShareNetMember" xlink:label="arwr_IssuedAtApproximatelyEighteenDollarPerShareNetMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="18" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedAtApproximatelyEighteenDollarPerShareNetMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedAtTwentySevenDollarsAndTwentyCentsPerShareToRiceUniversityMember" xlink:label="arwr_IssuedAtTwentySevenDollarsAndTwentyCentsPerShareToRiceUniversityMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="19" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedAtTwentySevenDollarsAndTwentyCentsPerShareToRiceUniversityMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedAtTwentyEightDollarsAndThirtyCentsPerShareToPurchaseSharesOfUnidymIncMember" xlink:label="arwr_IssuedAtTwentyEightDollarsAndThirtyCentsPerShareToPurchaseSharesOfUnidymIncMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="20" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedAtTwentyEightDollarsAndThirtyCentsPerShareToPurchaseSharesOfUnidymIncMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedAtTwentyNineDollarsAndFiftyCentsPerShareToPurchaseMasaEnergyLlcMember" xlink:label="arwr_IssuedAtTwentyNineDollarsAndFiftyCentsPerShareToPurchaseMasaEnergyLlcMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="21" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedAtTwentyNineDollarsAndFiftyCentsPerShareToPurchaseMasaEnergyLlcMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedAtTwentyOneDollarsAndNinetyCentsPerShareToUnidymForAcquisitionOfNanoconductionMember" xlink:label="arwr_IssuedAtTwentyOneDollarsAndNinetyCentsPerShareToUnidymForAcquisitionOfNanoconductionMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="22" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedAtTwentyOneDollarsAndNinetyCentsPerShareToUnidymForAcquisitionOfNanoconductionMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedAtTwentyOneDollarsAndEightyCentsPerShareMember" xlink:label="arwr_IssuedAtTwentyOneDollarsAndEightyCentsPerShareMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="23" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedAtTwentyOneDollarsAndEightyCentsPerShareMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedAtFiveDollarsAndFiftyCentsPerShareToUnidymStockholderInExchangeForUnidymSSharesMember" xlink:label="arwr_IssuedAtFiveDollarsAndFiftyCentsPerShareToUnidymStockholderInExchangeForUnidymSSharesMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="24" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedAtFiveDollarsAndFiftyCentsPerShareToUnidymStockholderInExchangeForUnidymSSharesMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedAtFiveDollarsAndTwentyCentsPerShareToTelVenturesInExchangeForUnidymSSharesMember" xlink:label="arwr_IssuedAtFiveDollarsAndTwentyCentsPerShareToTelVenturesInExchangeForUnidymSSharesMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="25" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedAtFiveDollarsAndTwentyCentsPerShareToTelVenturesInExchangeForUnidymSSharesMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedAtThreeDollarsPerShareMember" xlink:label="arwr_IssuedAtThreeDollarsPerShareMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="26" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedAtThreeDollarsPerShareMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedAtSixDollarsAndThirtyCentsPerShareMember" xlink:label="arwr_IssuedAtSixDollarsAndThirtyCentsPerShareMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="27" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedAtSixDollarsAndThirtyCentsPerShareMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedAtThirteenDollarsAndTwelveCentsPerShareMember" xlink:label="arwr_IssuedAtThirteenDollarsAndTwelveCentsPerShareMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="28" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedAtThirteenDollarsAndTwelveCentsPerShareMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_IssuedAtThreeDollarsAndEightyCentsPerShareMember" xlink:label="arwr_IssuedAtThreeDollarsAndEightyCentsPerShareMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="29" xlink:from="arwr_CommonStockIssuanceTypeDomain" xlink:to="arwr_IssuedAtThreeDollarsAndEightyCentsPerShareMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2011/elts/us-gaap-2011-01-31.xsd#us-gaap_StatementLineItems" xlink:label="us-gaap_StatementLineItems" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" order="1" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_StatementTable" use="optional" xbrldt:contextElement="segment" xbrldt:closed="true" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_CommonStockAndWarrantsIssuedForCashPricePerUnit" xlink:label="arwr_CommonStockAndWarrantsIssuedForCashPricePerUnit" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="2" xlink:from="us-gaap_StatementLineItems" xlink:to="arwr_CommonStockAndWarrantsIssuedForCashPricePerUnit" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_ExerciseOfStockOptionsPricePerShare" xlink:label="arwr_ExerciseOfStockOptionsPricePerShare" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="3" xlink:from="us-gaap_StatementLineItems" xlink:to="arwr_ExerciseOfStockOptionsPricePerShare" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_CommonStockIssuanceValuePerShare" xlink:label="arwr_CommonStockIssuanceValuePerShare" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="4" xlink:from="us-gaap_StatementLineItems" xlink:to="arwr_CommonStockIssuanceValuePerShare" priority="1" use="optional" />
  </definitionLink>
  <definitionLink xlink:role="http://www.arrowheadresearch.com/2010-06-30/role/StatementConsolidatedStatementsOfCashFlowsParenthetical" xlink:type="extended" xlink:title="00405 - Statement - Consolidated Statements Of Cash Flows (Parenthetical)">
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2011/elts/us-gaap-2011-01-31.xsd#us-gaap_StatementTable" xlink:label="us-gaap_StatementTable" />
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2011/elts/us-gaap-2011-01-31.xsd#us-gaap_StatementClassOfStockAxis" xlink:label="us-gaap_StatementClassOfStockAxis" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" order="1" xlink:from="us-gaap_StatementTable" xlink:to="us-gaap_StatementClassOfStockAxis" use="optional" />
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2011/elts/us-gaap-2011-01-31.xsd#us-gaap_ClassOfStockDomain" xlink:label="us-gaap_ClassOfStockDomain" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" order="1" xlink:from="us-gaap_StatementClassOfStockAxis" xlink:to="us-gaap_ClassOfStockDomain" use="optional" />
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2011/elts/us-gaap-2011-01-31.xsd#us-gaap_ClassOfStockDomain" xlink:label="us-gaap_ClassOfStockDomain_634599853593689409" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" order="1" xlink:from="us-gaap_StatementClassOfStockAxis" xlink:to="us-gaap_ClassOfStockDomain_634599853593689409" use="optional" />
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2011/elts/us-gaap-2011-01-31.xsd#us-gaap_SeriesEPreferredStockMember" xlink:label="us-gaap_SeriesEPreferredStockMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="1" xlink:from="us-gaap_ClassOfStockDomain" xlink:to="us-gaap_SeriesEPreferredStockMember" use="optional" />
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2011/elts/us-gaap-2011-01-31.xsd#us-gaap_SeriesAPreferredStockMember" xlink:label="us-gaap_SeriesAPreferredStockMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="2" xlink:from="us-gaap_ClassOfStockDomain" xlink:to="us-gaap_SeriesAPreferredStockMember" use="optional" />
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2011/elts/us-gaap-2011-01-31.xsd#us-gaap_SeriesCPreferredStockMember" xlink:label="us-gaap_SeriesCPreferredStockMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="3" xlink:from="us-gaap_ClassOfStockDomain" xlink:to="us-gaap_SeriesCPreferredStockMember" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_SeriesC1PreferredStockMember" xlink:label="arwr_SeriesC1PreferredStockMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="4" xlink:from="us-gaap_ClassOfStockDomain" xlink:to="arwr_SeriesC1PreferredStockMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="http://xbrl.sec.gov/dei/2011/dei-2011-01-31.xsd#dei_LegalEntityAxis" xlink:label="dei_LegalEntityAxis" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" order="2" xlink:from="us-gaap_StatementTable" xlink:to="dei_LegalEntityAxis" use="optional" />
    <loc xlink:type="locator" xlink:href="http://xbrl.sec.gov/dei/2011/dei-2011-01-31.xsd#dei_EntityDomain" xlink:label="dei_EntityDomain" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" order="1" xlink:from="dei_LegalEntityAxis" xlink:to="dei_EntityDomain" use="optional" />
    <loc xlink:type="locator" xlink:href="http://xbrl.sec.gov/dei/2011/dei-2011-01-31.xsd#dei_EntityDomain" xlink:label="dei_EntityDomain_634599853593689409" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" order="1" xlink:from="dei_LegalEntityAxis" xlink:to="dei_EntityDomain_634599853593689409" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_InsertTherapeuticsIncMember" xlink:label="arwr_InsertTherapeuticsIncMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="1" xlink:from="dei_EntityDomain" xlink:to="arwr_InsertTherapeuticsIncMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_CalandoPharmaceuticalsIncMember" xlink:label="arwr_CalandoPharmaceuticalsIncMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="2" xlink:from="dei_EntityDomain" xlink:to="arwr_CalandoPharmaceuticalsIncMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_CarbonNanotechnologiesIncMember" xlink:label="arwr_CarbonNanotechnologiesIncMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="3" xlink:from="dei_EntityDomain" xlink:to="arwr_CarbonNanotechnologiesIncMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_UnidymIncMember" xlink:label="arwr_UnidymIncMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="4" xlink:from="dei_EntityDomain" xlink:to="arwr_UnidymIncMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_MasaEnergyLlcMember" xlink:label="arwr_MasaEnergyLlcMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="5" xlink:from="dei_EntityDomain" xlink:to="arwr_MasaEnergyLlcMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_NanoconductionIncMember" xlink:label="arwr_NanoconductionIncMember" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="6" xlink:from="dei_EntityDomain" xlink:to="arwr_NanoconductionIncMember" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2011/elts/us-gaap-2011-01-31.xsd#us-gaap_StatementLineItems" xlink:label="us-gaap_StatementLineItems" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" order="1" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_StatementTable" use="optional" xbrldt:contextElement="segment" xbrldt:closed="true" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_CommonStockPurchasedFromMinorityShareHolders" xlink:label="arwr_CommonStockPurchasedFromMinorityShareHolders" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="2" xlink:from="us-gaap_StatementLineItems" xlink:to="arwr_CommonStockPurchasedFromMinorityShareHolders" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2011/elts/us-gaap-2011-01-31.xsd#us-gaap_CommonStockSharesIssued" xlink:label="us-gaap_CommonStockSharesIssued" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="3" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_CommonStockSharesIssued" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2011/elts/us-gaap-2011-01-31.xsd#us-gaap_CommonStockValue" xlink:label="us-gaap_CommonStockValue" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="4" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_CommonStockValue" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_ValueOfCommonStockPurchasedFromMinorityShareHolders" xlink:label="arwr_ValueOfCommonStockPurchasedFromMinorityShareHolders" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="5" xlink:from="us-gaap_StatementLineItems" xlink:to="arwr_ValueOfCommonStockPurchasedFromMinorityShareHolders" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_ValueOfCommonStockPurchasedByCash" xlink:label="arwr_ValueOfCommonStockPurchasedByCash" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="6" xlink:from="us-gaap_StatementLineItems" xlink:to="arwr_ValueOfCommonStockPurchasedByCash" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_WarrantsIssued" xlink:label="arwr_WarrantsIssued" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="7" xlink:from="us-gaap_StatementLineItems" xlink:to="arwr_WarrantsIssued" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_WarrantsPurchased" xlink:label="arwr_WarrantsPurchased" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="8" xlink:from="us-gaap_StatementLineItems" xlink:to="arwr_WarrantsPurchased" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_ExercisePriceOfWarrants" xlink:label="arwr_ExercisePriceOfWarrants" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="9" xlink:from="us-gaap_StatementLineItems" xlink:to="arwr_ExercisePriceOfWarrants" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_WarrantsExercised" xlink:label="arwr_WarrantsExercised" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="10" xlink:from="us-gaap_StatementLineItems" xlink:to="arwr_WarrantsExercised" priority="1" use="optional" />
    <loc xlink:type="locator" xlink:href="arwr-20110930.xsd#arwr_StockIssuedAgainstWarrants" xlink:label="arwr_StockIssuedAgainstWarrants" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" order="11" xlink:from="us-gaap_StatementLineItems" xlink:to="arwr_StockIssuedAgainstWarrants" priority="1" use="optional" />
  </definitionLink>
</linkbase>
