<?xml version="1.0" encoding="US-ASCII"?>
<!-- RR Donnelley Xcelerate Taxonomy Calculation Linkbase, based on XBRL 2.1  http://www.edgar-online.com/ -->
<!-- Version: 6.21.0 -->
<!-- Round: 7 -->
<!-- Creation date: 2014-08-07T18:02:47Z -->
<!-- Copyright (c) 2005-2013 R.R. Donnelley & Sons Company All Rights Reserved. -->
<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"
  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="ziop-20140630.xsd#DocumentandEntityInformation" roleURI="http://www.ziopharm.com/taxonomy/role/DocumentandEntityInformation"/>
  <roleRef xlink:type="simple" xlink:href="ziop-20140630.xsd#Role_StatementOfFinancialPositionClassified" roleURI="http://www.ziopharm.com/taxonomy/role/StatementOfFinancialPositionClassified"/>
  <roleRef xlink:type="simple" xlink:href="ziop-20140630.xsd#Role_StatementOfFinancialPositionClassifiedParen" roleURI="http://www.ziopharm.com/taxonomy/role/StatementOfFinancialPositionClassifiedParenthetical"/>
  <roleRef xlink:type="simple" xlink:href="ziop-20140630.xsd#Role_StatementOfIncomeAlternative" roleURI="http://www.ziopharm.com/taxonomy/role/StatementOfIncomeAlternative"/>
  <roleRef xlink:type="simple" xlink:href="ziop-20140630.xsd#Role_ci-StatementOfShareholdersEquityAndOtherComprehensiveIncome" roleURI="http://www.ziopharm.com/taxonomy/role/StatementOfShareholdersEquityAndOtherComprehensiveIncome"/>
  <roleRef xlink:type="simple" xlink:href="ziop-20140630.xsd#Role_StatementOfCashFlowsIndirect" roleURI="http://www.ziopharm.com/taxonomy/role/StatementOfCashFlowsIndirect"/>
  <roleRef xlink:type="simple" xlink:href="ziop-20140630.xsd#DisclosureBusinessAdditionalInformation" roleURI="http://www.ziopharm.com/taxonomy/role/DisclosureBusinessAdditionalInformation"/>
  <roleRef xlink:type="simple" xlink:href="ziop-20140630.xsd#DisclosureRestructuringAdditionalInformation" roleURI="http://www.ziopharm.com/taxonomy/role/DisclosureRestructuringAdditionalInformation"/>
  <roleRef xlink:type="simple" xlink:href="ziop-20140630.xsd#DisclosureAssetsAndLiabilitiesMeasuredAtFairValueOnRecurringBasis" roleURI="http://www.ziopharm.com/taxonomy/role/DisclosureAssetsAndLiabilitiesMeasuredAtFairValueOnRecurringBasis"/>
  <roleRef xlink:type="simple" xlink:href="ziop-20140630.xsd#DisclosurePotentialDilutiveSharesExcludedFromComputationOfDilutedNetLossPerShare" roleURI="http://www.ziopharm.com/taxonomy/role/DisclosurePotentialDilutiveSharesExcludedFromComputationOfDilutedNetLossPerShare"/>
  <roleRef xlink:type="simple" xlink:href="ziop-20140630.xsd#DisclosureRelatedPartyTransactionsAdditionalInformation" roleURI="http://www.ziopharm.com/taxonomy/role/DisclosureRelatedPartyTransactionsAdditionalInformation"/>
  <roleRef xlink:type="simple" xlink:href="ziop-20140630.xsd#DisclosureCommitmentsAndContingenciesAdditionalInformation" roleURI="http://www.ziopharm.com/taxonomy/role/DisclosureCommitmentsAndContingenciesAdditionalInformation"/>
  <roleRef xlink:type="simple" xlink:href="ziop-20140630.xsd#DisclosureNumberOfWarrantsOutstanding" roleURI="http://www.ziopharm.com/taxonomy/role/DisclosureNumberOfWarrantsOutstanding"/>
  <roleRef xlink:type="simple" xlink:href="ziop-20140630.xsd#DisclosureWarrantsAdditionalInformation" roleURI="http://www.ziopharm.com/taxonomy/role/DisclosureWarrantsAdditionalInformation"/>
  <roleRef xlink:type="simple" xlink:href="ziop-20140630.xsd#DisclosureAssumptionsUsedInBinomialValuationModelAndBlackScholesValuationModel" roleURI="http://www.ziopharm.com/taxonomy/role/DisclosureAssumptionsUsedInBinomialValuationModelAndBlackScholesValuationModel"/>
  <roleRef xlink:type="simple" xlink:href="ziop-20140630.xsd#DisclosureWarrantExercise" roleURI="http://www.ziopharm.com/taxonomy/role/DisclosureWarrantExercise"/>
  <roleRef xlink:type="simple" xlink:href="ziop-20140630.xsd#DisclosureCommonStockAdditionalInformation" roleURI="http://www.ziopharm.com/taxonomy/role/DisclosureCommonStockAdditionalInformation"/>
  <roleRef xlink:type="simple" xlink:href="ziop-20140630.xsd#DisclosureStockBasedCompensationExpenseOnAllEmployeeAndNonEmployeeAwards" roleURI="http://www.ziopharm.com/taxonomy/role/DisclosureStockBasedCompensationExpenseOnAllEmployeeAndNonEmployeeAwards"/>
  <roleRef xlink:type="simple" xlink:href="ziop-20140630.xsd#DisclosureStockBasedCompensationAdditionalInformation" roleURI="http://www.ziopharm.com/taxonomy/role/DisclosureStockBasedCompensationAdditionalInformation"/>
  <roleRef xlink:type="simple" xlink:href="ziop-20140630.xsd#DisclosureFairValueOfStockOptionsAssumptionsUsingBlackScholesOptionValuationModel" roleURI="http://www.ziopharm.com/taxonomy/role/DisclosureFairValueOfStockOptionsAssumptionsUsingBlackScholesOptionValuationModel"/>
  <roleRef xlink:type="simple" xlink:href="ziop-20140630.xsd#DisclosureStockOptionActivityUnderStockOptionPlan" roleURI="http://www.ziopharm.com/taxonomy/role/DisclosureStockOptionActivityUnderStockOptionPlan"/>
  <roleRef xlink:type="simple" xlink:href="ziop-20140630.xsd#DisclosureSummaryOfUnvestedRestrictedStock" roleURI="http://www.ziopharm.com/taxonomy/role/DisclosureSummaryOfUnvestedRestrictedStock"/>
  <roleRef xlink:type="simple" xlink:href="ziop-20140630.xsd#Role_NotesToFinancialStatementsBusinessDescriptionAndBasisOfPresentationTextBlock" roleURI="http://www.ziopharm.com/taxonomy/role/NotesToFinancialStatementsBusinessDescriptionAndBasisOfPresentationTextBlock"/>
  <roleRef xlink:type="simple" xlink:href="ziop-20140630.xsd#Role_NotesToFinancialStatementsSignificantAccountingPoliciesTextBlock" roleURI="http://www.ziopharm.com/taxonomy/role/NotesToFinancialStatementsSignificantAccountingPoliciesTextBlock"/>
  <roleRef xlink:type="simple" xlink:href="ziop-20140630.xsd#Role_NotesToFinancialStatementsDescriptionOfNewAccountingPronouncementsNotYetAdopted" roleURI="http://www.ziopharm.com/taxonomy/role/NotesToFinancialStatementsDescriptionOfNewAccountingPronouncementsNotYetAdopted"/>
  <roleRef xlink:type="simple" xlink:href="ziop-20140630.xsd#Role_NotesToFinancialStatementsRestructuringAndRelatedActivitiesDisclosureTextBlock" roleURI="http://www.ziopharm.com/taxonomy/role/NotesToFinancialStatementsRestructuringAndRelatedActivitiesDisclosureTextBlock"/>
  <roleRef xlink:type="simple" xlink:href="ziop-20140630.xsd#Role_NotesToFinancialStatementsFairValueMeasurementInputsDisclosureTextBlock" roleURI="http://www.ziopharm.com/taxonomy/role/NotesToFinancialStatementsFairValueMeasurementInputsDisclosureTextBlock"/>
  <roleRef xlink:type="simple" xlink:href="ziop-20140630.xsd#Role_NotesToFinancialStatementsFairValueMeasurementInputsDisclosureTextBlockTables" roleURI="http://www.ziopharm.com/taxonomy/role/NotesToFinancialStatementsFairValueMeasurementInputsDisclosureTextBlockTables"/>
  <roleRef xlink:type="simple" xlink:href="ziop-20140630.xsd#Role_NotesToFinancialStatementsEarningsPerShareTextBlock" roleURI="http://www.ziopharm.com/taxonomy/role/NotesToFinancialStatementsEarningsPerShareTextBlock"/>
  <roleRef xlink:type="simple" xlink:href="ziop-20140630.xsd#Role_NotesToFinancialStatementsEarningsPerShareTextBlockTables" roleURI="http://www.ziopharm.com/taxonomy/role/NotesToFinancialStatementsEarningsPerShareTextBlockTables"/>
  <roleRef xlink:type="simple" xlink:href="ziop-20140630.xsd#Role_NotesToFinancialStatementsRelatedPartyTransactionsDisclosureTextBlock" roleURI="http://www.ziopharm.com/taxonomy/role/NotesToFinancialStatementsRelatedPartyTransactionsDisclosureTextBlock"/>
  <roleRef xlink:type="simple" xlink:href="ziop-20140630.xsd#Role_NotesToFinancialStatementsCommitmentsAndContingenciesDisclosureTextBlock" roleURI="http://www.ziopharm.com/taxonomy/role/NotesToFinancialStatementsCommitmentsAndContingenciesDisclosureTextBlock"/>
  <roleRef xlink:type="simple" xlink:href="ziop-20140630.xsd#Role_NotesToFinancialStatementsStockWarrantsTextBlock" roleURI="http://www.ziopharm.com/taxonomy/role/NotesToFinancialStatementsStockWarrantsTextBlock"/>
  <roleRef xlink:type="simple" xlink:href="ziop-20140630.xsd#Role_NotesToFinancialStatementsStockWarrantsTextBlockTables" roleURI="http://www.ziopharm.com/taxonomy/role/NotesToFinancialStatementsStockWarrantsTextBlockTables"/>
  <roleRef xlink:type="simple" xlink:href="ziop-20140630.xsd#Role_NotesToFinancialStatementsCommonStockDisclosureTextBlock" roleURI="http://www.ziopharm.com/taxonomy/role/NotesToFinancialStatementsCommonStockDisclosureTextBlock"/>
  <roleRef xlink:type="simple" xlink:href="ziop-20140630.xsd#Role_NotesToFinancialStatementsDisclosureOfCompensationRelatedCostsShareBasedPaymentsTextBlock" roleURI="http://www.ziopharm.com/taxonomy/role/NotesToFinancialStatementsDisclosureOfCompensationRelatedCostsShareBasedPaymentsTextBlock"/>
  <roleRef xlink:type="simple" xlink:href="ziop-20140630.xsd#Role_NotesToFinancialStatementsDisclosureOfCompensationRelatedCostsShareBasedPaymentsTextBlockTables" roleURI="http://www.ziopharm.com/taxonomy/role/NotesToFinancialStatementsDisclosureOfCompensationRelatedCostsShareBasedPaymentsTextBlockTables"/>
  <calculationLink xlink:type="extended" xlink:role="http://www.ziopharm.com/taxonomy/role/DocumentandEntityInformation">
  </calculationLink>
  <calculationLink xlink:type="extended" xlink:role="http://www.ziopharm.com/taxonomy/role/StatementOfFinancialPositionClassified">
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_AccountsPayableCurrent" xlink:label="us-gaap_AccountsPayableCurrent"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_AccruedLiabilitiesCurrent" xlink:label="us-gaap_AccruedLiabilitiesCurrent"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_AdditionalPaidInCapitalCommonStock" xlink:label="us-gaap_AdditionalPaidInCapitalCommonStock"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_Assets" xlink:label="us-gaap_Assets"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_AssetsCurrent" xlink:label="us-gaap_AssetsCurrent"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_CashAndCashEquivalentsAtCarryingValue" xlink:label="us-gaap_CashAndCashEquivalentsAtCarryingValue"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_CommonStockValue" xlink:label="us-gaap_CommonStockValue"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_DeferredRentCreditCurrent" xlink:label="us-gaap_DeferredRentCreditCurrent"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_DeferredRentCreditNoncurrent" xlink:label="us-gaap_DeferredRentCreditNoncurrent"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_DeferredRevenueCurrent" xlink:label="us-gaap_DeferredRevenueCurrent"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_DeferredRevenueNoncurrent" xlink:label="us-gaap_DeferredRevenueNoncurrent"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_DepositsAssetsNoncurrent" xlink:label="us-gaap_DepositsAssetsNoncurrent"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_Liabilities" xlink:label="us-gaap_Liabilities"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_LiabilitiesAndStockholdersEquity" xlink:label="us-gaap_LiabilitiesAndStockholdersEquity"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_LiabilitiesCurrent" xlink:label="us-gaap_LiabilitiesCurrent"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_OtherAdditionalCapital" xlink:label="us-gaap_OtherAdditionalCapital"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_OtherAssetsNoncurrent" xlink:label="us-gaap_OtherAssetsNoncurrent"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_OtherLiabilitiesNoncurrent" xlink:label="us-gaap_OtherLiabilitiesNoncurrent"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_PreferredStockValue" xlink:label="us-gaap_PreferredStockValue"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_PrepaidExpenseAndOtherAssetsCurrent" xlink:label="us-gaap_PrepaidExpenseAndOtherAssetsCurrent"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_PropertyPlantAndEquipmentNet" xlink:label="us-gaap_PropertyPlantAndEquipmentNet"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_ReceivablesNetCurrent" xlink:label="us-gaap_ReceivablesNetCurrent"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_RetainedEarningsAccumulatedDeficit" xlink:label="us-gaap_RetainedEarningsAccumulatedDeficit"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_StockholdersEquity" xlink:label="us-gaap_StockholdersEquity"/>
    <loc xlink:type="locator" xlink:href="ziop-20140630.xsd#ziop_WarrantsLiability" xlink:label="ziop_WarrantsLiability"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Assets" xlink:to="us-gaap_AssetsCurrent" order="1.0400" weight="1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Assets" xlink:to="us-gaap_PropertyPlantAndEquipmentNet" order="1.0500" weight="1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Assets" xlink:to="us-gaap_DepositsAssetsNoncurrent" order="1.0600" weight="1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Assets" xlink:to="us-gaap_OtherAssetsNoncurrent" order="1.0700" weight="1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AssetsCurrent" xlink:to="us-gaap_CashAndCashEquivalentsAtCarryingValue" order="1.0100" weight="1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AssetsCurrent" xlink:to="us-gaap_ReceivablesNetCurrent" order="1.0200" weight="1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AssetsCurrent" xlink:to="us-gaap_PrepaidExpenseAndOtherAssetsCurrent" order="1.0300" weight="1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Liabilities" xlink:to="us-gaap_LiabilitiesCurrent" order="1.1200" weight="1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Liabilities" xlink:to="us-gaap_DeferredRevenueNoncurrent" order="1.1300" weight="1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Liabilities" xlink:to="us-gaap_DeferredRentCreditNoncurrent" order="1.1400" weight="1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Liabilities" xlink:to="ziop_WarrantsLiability" order="1.1500" weight="1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Liabilities" xlink:to="us-gaap_OtherLiabilitiesNoncurrent" order="1.1600" weight="1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesAndStockholdersEquity" xlink:to="us-gaap_Liabilities" order="1.1700" weight="1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesAndStockholdersEquity" xlink:to="us-gaap_StockholdersEquity" order="1.2300" weight="1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesCurrent" xlink:to="us-gaap_AccountsPayableCurrent" order="1.0800" weight="1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesCurrent" xlink:to="us-gaap_AccruedLiabilitiesCurrent" order="1.0900" weight="1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesCurrent" xlink:to="us-gaap_DeferredRevenueCurrent" order="1.1000" weight="1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesCurrent" xlink:to="us-gaap_DeferredRentCreditCurrent" order="1.1100" weight="1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_StockholdersEquity" xlink:to="us-gaap_PreferredStockValue" order="1.1800" weight="1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_StockholdersEquity" xlink:to="us-gaap_CommonStockValue" order="1.1900" weight="1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_StockholdersEquity" xlink:to="us-gaap_AdditionalPaidInCapitalCommonStock" order="1.2000" weight="1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_StockholdersEquity" xlink:to="us-gaap_OtherAdditionalCapital" order="1.2100" weight="1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_StockholdersEquity" xlink:to="us-gaap_RetainedEarningsAccumulatedDeficit" order="1.2200" weight="1.00" priority="2" use="optional"/>
  </calculationLink>
  <calculationLink xlink:type="extended" xlink:role="http://www.ziopharm.com/taxonomy/role/StatementOfFinancialPositionClassifiedParenthetical">
  </calculationLink>
  <calculationLink xlink:type="extended" xlink:role="http://www.ziopharm.com/taxonomy/role/StatementOfIncomeAlternative">
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_ContractsRevenue" xlink:label="us-gaap_ContractsRevenue"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_GeneralAndAdministrativeExpense" xlink:label="us-gaap_GeneralAndAdministrativeExpense"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_NetIncomeLoss" xlink:label="us-gaap_NetIncomeLoss"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_OperatingCostsAndExpenses" xlink:label="us-gaap_OperatingCostsAndExpenses"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_OperatingIncomeLoss" xlink:label="us-gaap_OperatingIncomeLoss"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_OtherNonoperatingIncomeExpense" xlink:label="us-gaap_OtherNonoperatingIncomeExpense"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_ResearchAndDevelopmentExpense" xlink:label="us-gaap_ResearchAndDevelopmentExpense"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_UnrealizedGainLossOnDerivatives" xlink:label="us-gaap_UnrealizedGainLossOnDerivatives"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetIncomeLoss" xlink:to="us-gaap_OperatingIncomeLoss" order="1.0500" weight="1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetIncomeLoss" xlink:to="us-gaap_OtherNonoperatingIncomeExpense" order="1.0600" weight="1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetIncomeLoss" xlink:to="us-gaap_UnrealizedGainLossOnDerivatives" order="1.0700" weight="1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OperatingCostsAndExpenses" xlink:to="us-gaap_ResearchAndDevelopmentExpense" order="1.0200" weight="1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OperatingCostsAndExpenses" xlink:to="us-gaap_GeneralAndAdministrativeExpense" order="1.0300" weight="1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OperatingIncomeLoss" xlink:to="us-gaap_ContractsRevenue" order="1.0100" weight="1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OperatingIncomeLoss" xlink:to="us-gaap_OperatingCostsAndExpenses" order="1.0400" weight="-1.00" priority="2" use="optional"/>
  </calculationLink>
  <calculationLink xlink:type="extended" xlink:role="http://www.ziopharm.com/taxonomy/role/StatementOfShareholdersEquityAndOtherComprehensiveIncome">
  </calculationLink>
  <calculationLink xlink:type="extended" xlink:role="http://www.ziopharm.com/taxonomy/role/StatementOfCashFlowsIndirect">
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_CashAndCashEquivalentsPeriodIncreaseDecrease" xlink:label="us-gaap_CashAndCashEquivalentsPeriodIncreaseDecrease"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_DepreciationAndAmortization" xlink:label="us-gaap_DepreciationAndAmortization"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_IncreaseDecreaseInAccountsPayable" xlink:label="us-gaap_IncreaseDecreaseInAccountsPayable"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_IncreaseDecreaseInAccruedLiabilities" xlink:label="us-gaap_IncreaseDecreaseInAccruedLiabilities"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_IncreaseDecreaseInDeferredRevenue" xlink:label="us-gaap_IncreaseDecreaseInDeferredRevenue"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_IncreaseDecreaseInDepositOtherAssets" xlink:label="us-gaap_IncreaseDecreaseInDepositOtherAssets"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_IncreaseDecreaseInOtherDeferredLiability" xlink:label="us-gaap_IncreaseDecreaseInOtherDeferredLiability"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_IncreaseDecreaseInOtherNoncurrentAssets" xlink:label="us-gaap_IncreaseDecreaseInOtherNoncurrentAssets"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_IncreaseDecreaseInPrepaidDeferredExpenseAndOtherAssets" xlink:label="us-gaap_IncreaseDecreaseInPrepaidDeferredExpenseAndOtherAssets"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_IncreaseDecreaseInReceivables" xlink:label="us-gaap_IncreaseDecreaseInReceivables"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_NetCashProvidedByUsedInFinancingActivitiesContinuingOperations" xlink:label="us-gaap_NetCashProvidedByUsedInFinancingActivitiesContinuingOperations"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_NetCashProvidedByUsedInInvestingActivitiesContinuingOperations" xlink:label="us-gaap_NetCashProvidedByUsedInInvestingActivitiesContinuingOperations"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_NetCashProvidedByUsedInOperatingActivitiesContinuingOperations" xlink:label="us-gaap_NetCashProvidedByUsedInOperatingActivitiesContinuingOperations"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_NetIncomeLoss" xlink:label="us-gaap_NetIncomeLoss"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_PaymentsForRepurchaseOfCommonStock" xlink:label="us-gaap_PaymentsForRepurchaseOfCommonStock"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_PaymentsToAcquirePropertyPlantAndEquipment" xlink:label="us-gaap_PaymentsToAcquirePropertyPlantAndEquipment"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_ProceedsFromStockOptionsExercised" xlink:label="us-gaap_ProceedsFromStockOptionsExercised"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_ProceedsFromWarrantExercises" xlink:label="us-gaap_ProceedsFromWarrantExercises"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_ShareBasedCompensation" xlink:label="us-gaap_ShareBasedCompensation"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd#us-gaap_UnrealizedGainLossOnDerivatives" xlink:label="us-gaap_UnrealizedGainLossOnDerivatives"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_CashAndCashEquivalentsPeriodIncreaseDecrease" xlink:to="us-gaap_NetCashProvidedByUsedInOperatingActivitiesContinuingOperations" order="1.1300" weight="1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_CashAndCashEquivalentsPeriodIncreaseDecrease" xlink:to="us-gaap_NetCashProvidedByUsedInInvestingActivitiesContinuingOperations" order="1.1500" weight="1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_CashAndCashEquivalentsPeriodIncreaseDecrease" xlink:to="us-gaap_NetCashProvidedByUsedInFinancingActivitiesContinuingOperations" order="1.1900" weight="1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInFinancingActivitiesContinuingOperations" xlink:to="us-gaap_ProceedsFromStockOptionsExercised" order="1.1600" weight="1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInFinancingActivitiesContinuingOperations" xlink:to="us-gaap_PaymentsForRepurchaseOfCommonStock" order="1.1700" weight="-1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInFinancingActivitiesContinuingOperations" xlink:to="us-gaap_ProceedsFromWarrantExercises" order="1.1800" weight="1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInInvestingActivitiesContinuingOperations" xlink:to="us-gaap_PaymentsToAcquirePropertyPlantAndEquipment" order="1.1400" weight="-1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivitiesContinuingOperations" xlink:to="us-gaap_NetIncomeLoss" order="1.0100" weight="1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivitiesContinuingOperations" xlink:to="us-gaap_DepreciationAndAmortization" order="1.0200" weight="1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivitiesContinuingOperations" xlink:to="us-gaap_ShareBasedCompensation" order="1.0300" weight="1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivitiesContinuingOperations" xlink:to="us-gaap_UnrealizedGainLossOnDerivatives" order="1.0400" weight="-1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivitiesContinuingOperations" xlink:to="us-gaap_IncreaseDecreaseInReceivables" order="1.0500" weight="-1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivitiesContinuingOperations" xlink:to="us-gaap_IncreaseDecreaseInPrepaidDeferredExpenseAndOtherAssets" order="1.0600" weight="-1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivitiesContinuingOperations" xlink:to="us-gaap_IncreaseDecreaseInOtherNoncurrentAssets" order="1.0700" weight="-1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivitiesContinuingOperations" xlink:to="us-gaap_IncreaseDecreaseInDepositOtherAssets" order="1.0800" weight="-1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivitiesContinuingOperations" xlink:to="us-gaap_IncreaseDecreaseInAccountsPayable" order="1.0900" weight="1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivitiesContinuingOperations" xlink:to="us-gaap_IncreaseDecreaseInAccruedLiabilities" order="1.1000" weight="1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivitiesContinuingOperations" xlink:to="us-gaap_IncreaseDecreaseInDeferredRevenue" order="1.1100" weight="1.00" priority="2" use="optional"/>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivitiesContinuingOperations" xlink:to="us-gaap_IncreaseDecreaseInOtherDeferredLiability" order="1.1200" weight="1.00" priority="2" use="optional"/>
  </calculationLink>
  <calculationLink xlink:type="extended" xlink:role="http://www.ziopharm.com/taxonomy/role/DisclosureBusinessAdditionalInformation">
  </calculationLink>
  <calculationLink xlink:type="extended" xlink:role="http://www.ziopharm.com/taxonomy/role/DisclosureRestructuringAdditionalInformation">
  </calculationLink>
  <calculationLink xlink:type="extended" xlink:role="http://www.ziopharm.com/taxonomy/role/DisclosureAssetsAndLiabilitiesMeasuredAtFairValueOnRecurringBasis">
  </calculationLink>
  <calculationLink xlink:type="extended" xlink:role="http://www.ziopharm.com/taxonomy/role/DisclosurePotentialDilutiveSharesExcludedFromComputationOfDilutedNetLossPerShare">
  </calculationLink>
  <calculationLink xlink:type="extended" xlink:role="http://www.ziopharm.com/taxonomy/role/DisclosureRelatedPartyTransactionsAdditionalInformation">
  </calculationLink>
  <calculationLink xlink:type="extended" xlink:role="http://www.ziopharm.com/taxonomy/role/DisclosureCommitmentsAndContingenciesAdditionalInformation">
  </calculationLink>
  <calculationLink xlink:type="extended" xlink:role="http://www.ziopharm.com/taxonomy/role/DisclosureNumberOfWarrantsOutstanding">
  </calculationLink>
  <calculationLink xlink:type="extended" xlink:role="http://www.ziopharm.com/taxonomy/role/DisclosureWarrantsAdditionalInformation">
  </calculationLink>
  <calculationLink xlink:type="extended" xlink:role="http://www.ziopharm.com/taxonomy/role/DisclosureAssumptionsUsedInBinomialValuationModelAndBlackScholesValuationModel">
  </calculationLink>
  <calculationLink xlink:type="extended" xlink:role="http://www.ziopharm.com/taxonomy/role/DisclosureWarrantExercise">
  </calculationLink>
  <calculationLink xlink:type="extended" xlink:role="http://www.ziopharm.com/taxonomy/role/DisclosureCommonStockAdditionalInformation">
  </calculationLink>
  <calculationLink xlink:type="extended" xlink:role="http://www.ziopharm.com/taxonomy/role/DisclosureStockBasedCompensationExpenseOnAllEmployeeAndNonEmployeeAwards">
  </calculationLink>
  <calculationLink xlink:type="extended" xlink:role="http://www.ziopharm.com/taxonomy/role/DisclosureStockBasedCompensationAdditionalInformation">
  </calculationLink>
  <calculationLink xlink:type="extended" xlink:role="http://www.ziopharm.com/taxonomy/role/DisclosureFairValueOfStockOptionsAssumptionsUsingBlackScholesOptionValuationModel">
  </calculationLink>
  <calculationLink xlink:type="extended" xlink:role="http://www.ziopharm.com/taxonomy/role/DisclosureStockOptionActivityUnderStockOptionPlan">
  </calculationLink>
  <calculationLink xlink:type="extended" xlink:role="http://www.ziopharm.com/taxonomy/role/DisclosureSummaryOfUnvestedRestrictedStock">
  </calculationLink>
  <calculationLink xlink:type="extended" xlink:role="http://www.ziopharm.com/taxonomy/role/NotesToFinancialStatementsBusinessDescriptionAndBasisOfPresentationTextBlock">
  </calculationLink>
  <calculationLink xlink:type="extended" xlink:role="http://www.ziopharm.com/taxonomy/role/NotesToFinancialStatementsSignificantAccountingPoliciesTextBlock">
  </calculationLink>
  <calculationLink xlink:type="extended" xlink:role="http://www.ziopharm.com/taxonomy/role/NotesToFinancialStatementsDescriptionOfNewAccountingPronouncementsNotYetAdopted">
  </calculationLink>
  <calculationLink xlink:type="extended" xlink:role="http://www.ziopharm.com/taxonomy/role/NotesToFinancialStatementsRestructuringAndRelatedActivitiesDisclosureTextBlock">
  </calculationLink>
  <calculationLink xlink:type="extended" xlink:role="http://www.ziopharm.com/taxonomy/role/NotesToFinancialStatementsFairValueMeasurementInputsDisclosureTextBlock">
  </calculationLink>
  <calculationLink xlink:type="extended" xlink:role="http://www.ziopharm.com/taxonomy/role/NotesToFinancialStatementsFairValueMeasurementInputsDisclosureTextBlockTables">
  </calculationLink>
  <calculationLink xlink:type="extended" xlink:role="http://www.ziopharm.com/taxonomy/role/NotesToFinancialStatementsEarningsPerShareTextBlock">
  </calculationLink>
  <calculationLink xlink:type="extended" xlink:role="http://www.ziopharm.com/taxonomy/role/NotesToFinancialStatementsEarningsPerShareTextBlockTables">
  </calculationLink>
  <calculationLink xlink:type="extended" xlink:role="http://www.ziopharm.com/taxonomy/role/NotesToFinancialStatementsRelatedPartyTransactionsDisclosureTextBlock">
  </calculationLink>
  <calculationLink xlink:type="extended" xlink:role="http://www.ziopharm.com/taxonomy/role/NotesToFinancialStatementsCommitmentsAndContingenciesDisclosureTextBlock">
  </calculationLink>
  <calculationLink xlink:type="extended" xlink:role="http://www.ziopharm.com/taxonomy/role/NotesToFinancialStatementsStockWarrantsTextBlock">
  </calculationLink>
  <calculationLink xlink:type="extended" xlink:role="http://www.ziopharm.com/taxonomy/role/NotesToFinancialStatementsStockWarrantsTextBlockTables">
  </calculationLink>
  <calculationLink xlink:type="extended" xlink:role="http://www.ziopharm.com/taxonomy/role/NotesToFinancialStatementsCommonStockDisclosureTextBlock">
  </calculationLink>
  <calculationLink xlink:type="extended" xlink:role="http://www.ziopharm.com/taxonomy/role/NotesToFinancialStatementsDisclosureOfCompensationRelatedCostsShareBasedPaymentsTextBlock">
  </calculationLink>
  <calculationLink xlink:type="extended" xlink:role="http://www.ziopharm.com/taxonomy/role/NotesToFinancialStatementsDisclosureOfCompensationRelatedCostsShareBasedPaymentsTextBlockTables">
  </calculationLink>
</linkbase>


