<?xml version="1.0" encoding="US-ASCII"?>
<!-- RR Donnelley Xcelerate Taxonomy Schema, based on XBRL 2.1  http://www.rrdonnelley.com/ -->
<!-- Version: 6.21.0 -->
<!-- Round: 6 -->
<!-- Creation date: 2014-08-08T20:59:13Z -->
<!-- Copyright (c) 2005-2013 R.R. Donnelley & Sons Company All Rights Reserved. -->
<schema xmlns="http://www.w3.org/2001/XMLSchema"
  xmlns:xbrli="http://www.xbrl.org/2003/instance"
  xmlns:link="http://www.xbrl.org/2003/linkbase"
  xmlns:xlink="http://www.w3.org/1999/xlink"
  xmlns:us-gaap="http://fasb.org/us-gaap/2013-01-31"
  xmlns:us-types="http://fasb.org/us-types/2013-01-31"
  xmlns:idra="http://www.iderapharma.com/20140630"
  xmlns:nonnum="http://www.xbrl.org/dtr/type/non-numeric"
  xmlns:num="http://www.xbrl.org/dtr/type/numeric"
  xmlns:xbrldt="http://xbrl.org/2005/xbrldt"
  xmlns:country="http://xbrl.sec.gov/country/2013-01-31"
  xmlns:currency="http://xbrl.sec.gov/currency/2012-01-31"
  xmlns:dei="http://xbrl.sec.gov/dei/2013-01-31"
  xmlns:exch="http://xbrl.sec.gov/exch/2013-01-31"
  xmlns:invest="http://xbrl.sec.gov/invest/2013-01-31"
  xmlns:stpr="http://xbrl.sec.gov/stpr/2011-01-31"
  targetNamespace="http://www.iderapharma.com/20140630"
  elementFormDefault="qualified" attributeFormDefault="unqualified">
  <annotation>
    <appinfo>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/DocumentandEntityInformation" id="DocumentandEntityInformation">
        <link:definition>101 - Document - Document and Entity Information</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/StatementOfFinancialPositionClassified" id="Role_StatementOfFinancialPositionClassified">
        <link:definition>103 - Statement - Condensed Balance Sheets (Unaudited)</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/StatementOfFinancialPositionClassifiedParenthetical" id="Role_StatementOfFinancialPositionClassifiedParen">
        <link:definition>104 - Statement - Condensed Balance Sheets (Unaudited) (Parenthetical)</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/StatementOfIncome" id="Role_StatementOfIncome">
        <link:definition>105 - Statement - Condensed Statements of Operations and Comprehensive Loss (Unaudited)</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/StatementOfCashFlowsIndirect" id="Role_StatementOfCashFlowsIndirect">
        <link:definition>106 - Statement - Condensed Statements of Cash Flows (Unaudited)</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/NotesToFinancialStatementsOrganizationConsolidationAndPresentationOfFinancialStatementsDisclosureTextBlock" id="Role_NotesToFinancialStatementsOrganizationConsolidationAndPresentationOfFinancialStatementsDisclosureTextBlock">
        <link:definition>107 - Disclosure - Organization</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/NotesToFinancialStatementsNewAccountingPronouncementsAndChangesInAccountingPrinciplesTextBlock" id="Role_NotesToFinancialStatementsNewAccountingPronouncementsAndChangesInAccountingPrinciplesTextBlock">
        <link:definition>108 - Disclosure - New Accounting Pronouncements - Recently Issued</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/NotesToFinancialStatementsCondensedFinancialStatementsTextBlock" id="Role_NotesToFinancialStatementsCondensedFinancialStatementsTextBlock">
        <link:definition>109 - Disclosure - Unaudited Interim Financial Statements</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/NotesToFinancialStatementsFinancialInstrumentsDisclosureTextBlock" id="Role_NotesToFinancialStatementsFinancialInstrumentsDisclosureTextBlock">
        <link:definition>110 - Disclosure - Financial Instruments</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/NotesToFinancialStatementsCashAndCashEquivalentsDisclosureTextBlock" id="Role_NotesToFinancialStatementsCashAndCashEquivalentsDisclosureTextBlock">
        <link:definition>111 - Disclosure - Cash and Cash Equivalents</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/NotesToFinancialStatementsFairValueDisclosuresTextBlock" id="Role_NotesToFinancialStatementsFairValueDisclosuresTextBlock">
        <link:definition>112 - Disclosure - Fair Value of Assets and Liabilities</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/NotesToFinancialStatementsInvestmentsInDebtAndMarketableEquitySecuritiesAndCertainTradingAssetsDisclosureTextBlock" id="Role_NotesToFinancialStatementsInvestmentsInDebtAndMarketableEquitySecuritiesAndCertainTradingAssetsDisclosureTextBlock">
        <link:definition>113 - Disclosure - Investments</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/NotesToFinancialStatementsPropertyPlantAndEquipmentDisclosureTextBlock" id="Role_NotesToFinancialStatementsPropertyPlantAndEquipmentDisclosureTextBlock">
        <link:definition>114 - Disclosure - Property and Equipment</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/NotesToFinancialStatementsRestrictedAssetsDisclosureTextBlock" id="Role_NotesToFinancialStatementsRestrictedAssetsDisclosureTextBlock">
        <link:definition>115 - Disclosure - Restricted Cash</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/NotesToFinancialStatementsCollaborativeArrangementDisclosureTextBlock" id="Role_NotesToFinancialStatementsCollaborativeArrangementDisclosureTextBlock">
        <link:definition>116 - Disclosure - Collaborations</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/NotesToFinancialStatementsComprehensiveIncomeNoteTextBlock" id="Role_NotesToFinancialStatementsComprehensiveIncomeNoteTextBlock">
        <link:definition>117 - Disclosure - Comprehensive Income (Loss)</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/NotesToFinancialStatementsDisclosureOfCompensationRelatedCostsShareBasedPaymentsTextBlock" id="Role_NotesToFinancialStatementsDisclosureOfCompensationRelatedCostsShareBasedPaymentsTextBlock">
        <link:definition>118 - Disclosure - Stock-Based Compensation</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/NotesToFinancialStatementsEarningsPerShareTextBlock" id="Role_NotesToFinancialStatementsEarningsPerShareTextBlock">
        <link:definition>119 - Disclosure - Net Loss per Common Share Applicable to Common Stockholders</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/NotesToFinancialStatementsCommonStockWarrantAndOptionExercisesAndEmployeeStockPurchasesTextBlock" id="Role_NotesToFinancialStatementsCommonStockWarrantAndOptionExercisesAndEmployeeStockPurchasesTextBlock">
        <link:definition>120 - Disclosure - Common Stock Warrant and Option Exercises and Employee Stock Purchases</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/NotesToFinancialStatementsRelatedPartyTransactionsDisclosureTextBlock" id="Role_NotesToFinancialStatementsRelatedPartyTransactionsDisclosureTextBlock">
        <link:definition>121 - Disclosure - Related Party Transactions</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/NotesToFinancialStatementsSaleOfCommonAndPreferredStockAndWarrantsTextBlock" id="Role_NotesToFinancialStatementsSaleOfCommonAndPreferredStockAndWarrantsTextBlock">
        <link:definition>122 - Disclosure - Financing</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/NotesToFinancialStatementsSubsequentEventsTextBlock" id="Role_NotesToFinancialStatementsSubsequentEventsTextBlock">
        <link:definition>123 - Disclosure - Subsequent Events</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/NotesToFinancialStatementsNewAccountingPronouncementsAndChangesInAccountingPrinciplesTextBlockPolicies" id="Role_NotesToFinancialStatementsNewAccountingPronouncementsAndChangesInAccountingPrinciplesTextBlockPolicies">
        <link:definition>124 - Disclosure - New Accounting Pronouncements - Recently Issued (Policies)</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/NotesToFinancialStatementsFairValueDisclosuresTextBlockTables" id="Role_NotesToFinancialStatementsFairValueDisclosuresTextBlockTables">
        <link:definition>125 - Disclosure - Fair Value of Assets and Liabilities (Tables)</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/NotesToFinancialStatementsInvestmentsInDebtAndMarketableEquitySecuritiesAndCertainTradingAssetsDisclosureTextBlockTables" id="Role_NotesToFinancialStatementsInvestmentsInDebtAndMarketableEquitySecuritiesAndCertainTradingAssetsDisclosureTextBlockTables">
        <link:definition>126 - Disclosure - Investments (Tables)</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/NotesToFinancialStatementsPropertyPlantAndEquipmentDisclosureTextBlockTables" id="Role_NotesToFinancialStatementsPropertyPlantAndEquipmentDisclosureTextBlockTables">
        <link:definition>127 - Disclosure - Property and Equipment (Tables)</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/NotesToFinancialStatementsComprehensiveIncomeNoteTextBlockTables" id="Role_NotesToFinancialStatementsComprehensiveIncomeNoteTextBlockTables">
        <link:definition>128 - Disclosure - Comprehensive Income (Loss) (Tables)</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/NotesToFinancialStatementsDisclosureOfCompensationRelatedCostsShareBasedPaymentsTextBlockTables" id="Role_NotesToFinancialStatementsDisclosureOfCompensationRelatedCostsShareBasedPaymentsTextBlockTables">
        <link:definition>129 - Disclosure - Stock-Based Compensation (Tables)</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/NotesToFinancialStatementsSaleOfCommonAndPreferredStockAndWarrantsTextBlockTables" id="Role_NotesToFinancialStatementsSaleOfCommonAndPreferredStockAndWarrantsTextBlockTables">
        <link:definition>130 - Disclosure - Financing (Tables)</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/DisclosureOrganizationAdditionalInformation" id="DisclosureOrganizationAdditionalInformation">
        <link:definition>131 - Disclosure - Organization - Additional Information (Detail)</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/DisclosureCashAndCashEquivalentsAdditionalInformation" id="DisclosureCashAndCashEquivalentsAdditionalInformation">
        <link:definition>132 - Disclosure - Cash and Cash Equivalents - Additional Information (Detail)</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/DisclosureFairValueOfAssetsAndLiabilitiesAssetsAndLiabilitiesMeasuredAtFairValueOnARecurringBasis" id="DisclosureFairValueOfAssetsAndLiabilitiesAssetsAndLiabilitiesMeasuredAtFairValueOnARecurringBasis">
        <link:definition>133 - Disclosure - Fair Value of Assets and Liabilities - Assets and Liabilities Measured at Fair Value on a Recurring Basis (Detail)</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/DisclosureInvestmentsSummaryOfAvailableforSaleInvestmentsAtFairValue" id="DisclosureInvestmentsSummaryOfAvailableforSaleInvestmentsAtFairValue">
        <link:definition>134 - Disclosure - Investments - Summary of Available-for-Sale Investments at Fair Value (Detail)</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/DisclosureInvestmentsAdditionalInformation" id="DisclosureInvestmentsAdditionalInformation">
        <link:definition>135 - Disclosure - Investments - Additional Information (Detail)</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/DisclosurePropertyAndEquipmentTabularDisclosureOfMajorComponentsOfPropertyAndEquipmentAndRelatedAccumulatedDepreciation" id="DisclosurePropertyAndEquipmentTabularDisclosureOfMajorComponentsOfPropertyAndEquipmentAndRelatedAccumulatedDepreciation">
        <link:definition>136 - Disclosure - Property and Equipment - Tabular Disclosure of Major Components of Property and Equipment and Related Accumulated Depreciation (Detail)</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/DisclosurePropertyAndEquipmentAdditionalInformation" id="DisclosurePropertyAndEquipmentAdditionalInformation">
        <link:definition>137 - Disclosure - Property and Equipment - Additional Information (Detail)</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/DisclosureRestrictedCashAdditionalInformation" id="DisclosureRestrictedCashAdditionalInformation">
        <link:definition>138 - Disclosure - Restricted Cash - Additional Information (Detail)</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/DisclosureCollaborationsAdditionalInformation" id="DisclosureCollaborationsAdditionalInformation">
        <link:definition>139 - Disclosure - Collaborations - Additional Information (Detail)</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/DisclosureComprehensiveIncomeLossChangesInAccumulatedBalanceOfTheComponentOfOtherComprehensiveGainLoss" id="DisclosureComprehensiveIncomeLossChangesInAccumulatedBalanceOfTheComponentOfOtherComprehensiveGainLoss">
        <link:definition>140 - Disclosure - Comprehensive Income (Loss) - Changes in Accumulated Balance of the Component of Other Comprehensive Gain (Loss) (Detail)</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/DisclosureComprehensiveIncomeLossAdditionalInformation" id="DisclosureComprehensiveIncomeLossAdditionalInformation">
        <link:definition>141 - Disclosure - Comprehensive Income (Loss) - Additional Information (Detail)</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/DisclosureStockBasedCompensationAdditionalInformation" id="DisclosureStockBasedCompensationAdditionalInformation">
        <link:definition>142 - Disclosure - Stock-Based Compensation - Additional Information (Detail)</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/DisclosureStockBasedCompensationScheduleOfAssumptionsUsedToDetermineFairValueOfStockOptionsGrantedDuringPeriod" id="DisclosureStockBasedCompensationScheduleOfAssumptionsUsedToDetermineFairValueOfStockOptionsGrantedDuringPeriod">
        <link:definition>143 - Disclosure - Stock-Based Compensation - Schedule of Assumptions Used to Determine Fair Value of Stock Options Granted During Period (Detail)</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/DisclosureNetLossPerCommonShareApplicableToCommonStockholdersAdditionalInformation" id="DisclosureNetLossPerCommonShareApplicableToCommonStockholdersAdditionalInformation">
        <link:definition>144 - Disclosure - Net Loss per Common Share Applicable to Common Stockholders - Additional Information (Detail)</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/DisclosureCommonStockWarrantAndOptionExercisesAndEmployeeStockPurchasesAdditionalInformation" id="DisclosureCommonStockWarrantAndOptionExercisesAndEmployeeStockPurchasesAdditionalInformation">
        <link:definition>145 - Disclosure - Common Stock Warrant and Option Exercises and Employee Stock Purchases - Additional Information (Detail)</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/DisclosureRelatedPartyTransactionsAdditionalInformation" id="DisclosureRelatedPartyTransactionsAdditionalInformation">
        <link:definition>146 - Disclosure - Related Party Transactions - Additional Information (Detail)</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/DisclosureFinancingAdditionalInformation1" id="DisclosureFinancingAdditionalInformation1">
        <link:definition>147 - Disclosure - Financing - Additional Information 1 (Detail)</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/DisclosureFinancingAdditionalInformation2" id="DisclosureFinancingAdditionalInformation2">
        <link:definition>148 - Disclosure - Financing - Additional Information 2 (Detail)</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/DisclosureFinancingMay2013FollowonUnderwrittenPublicOffering" id="DisclosureFinancingMay2013FollowonUnderwrittenPublicOffering">
        <link:definition>149 - Disclosure - Financing - May 2013 Follow-on Underwritten Public Offering (Detail)</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.iderapharma.com/taxonomy/role/DisclosureFinancingAdditionalInformation3" id="DisclosureFinancingAdditionalInformation3">
        <link:definition>150 - Disclosure - Financing - Additional Information 3 (Detail)</link:definition>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:linkbaseRef xlink:type="simple" xlink:arcrole="http://www.w3.org/1999/xlink/properties/linkbase" xlink:role="http://www.xbrl.org/2003/role/calculationLinkbaseRef" xlink:href="idra-20140630_cal.xml" xlink:title="Calculation Links, all"/>
      <link:linkbaseRef xlink:type="simple" xlink:arcrole="http://www.w3.org/1999/xlink/properties/linkbase" xlink:role="http://www.xbrl.org/2003/role/definitionLinkbaseRef" xlink:href="idra-20140630_def.xml" xlink:title="Definition Links, all"/>
      <link:linkbaseRef xlink:type="simple" xlink:arcrole="http://www.w3.org/1999/xlink/properties/linkbase" xlink:role="http://www.xbrl.org/2003/role/labelLinkbaseRef" xlink:href="idra-20140630_lab.xml" xlink:title="Label Links, all"/>
      <link:linkbaseRef xlink:type="simple" xlink:arcrole="http://www.w3.org/1999/xlink/properties/linkbase" xlink:role="http://www.xbrl.org/2003/role/presentationLinkbaseRef" xlink:href="idra-20140630_pre.xml" xlink:title="Presentation Links, all"/>
    </appinfo>
  </annotation>
  <import namespace="http://www.xbrl.org/2003/instance" schemaLocation="http://www.xbrl.org/2003/xbrl-instance-2003-12-31.xsd"/>
  <import namespace="http://www.xbrl.org/2003/linkbase" schemaLocation="http://www.xbrl.org/2003/xbrl-linkbase-2003-12-31.xsd"/>
  <import namespace="http://xbrl.org/2005/xbrldt" schemaLocation="http://www.xbrl.org/2005/xbrldt-2005.xsd"/>
  <import namespace="http://fasb.org/us-types/2013-01-31" schemaLocation="http://xbrl.fasb.org/us-gaap/2013/elts/us-types-2013-01-31.xsd"/>
  <import namespace="http://www.xbrl.org/dtr/type/numeric" schemaLocation="http://www.xbrl.org/dtr/type/numeric-2009-12-16.xsd"/>
  <import namespace="http://www.xbrl.org/dtr/type/non-numeric" schemaLocation="http://www.xbrl.org/dtr/type/nonNumeric-2009-12-16.xsd"/>
  <import namespace="http://fasb.org/us-gaap/2013-01-31" schemaLocation="http://xbrl.fasb.org/us-gaap/2013/elts/us-gaap-2013-01-31.xsd"/>
  <import namespace="http://xbrl.sec.gov/country/2013-01-31" schemaLocation="http://xbrl.sec.gov/country/2013/country-2013-01-31.xsd"/>
  <import namespace="http://xbrl.sec.gov/currency/2012-01-31" schemaLocation="http://xbrl.sec.gov/currency/2012/currency-2012-01-31.xsd"/>
  <import namespace="http://xbrl.sec.gov/dei/2013-01-31" schemaLocation="http://xbrl.sec.gov/dei/2013/dei-2013-01-31.xsd"/>
  <import namespace="http://xbrl.sec.gov/exch/2013-01-31" schemaLocation="http://xbrl.sec.gov/exch/2013/exch-2013-01-31.xsd"/>
  <import namespace="http://xbrl.sec.gov/invest/2013-01-31" schemaLocation="http://xbrl.sec.gov/invest/2013/invest-2013-01-31.xsd"/>
  <import namespace="http://xbrl.sec.gov/stpr/2011-01-31" schemaLocation="http://xbrl.sec.gov/stpr/2011/stpr-2011-01-31.xsd"/>
  <element name="AbbottMolecularMember" id="idra_AbbottMolecularMember" type="nonnum:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="AvailableForSaleSecuritiesGrossUnrealizedGainsAccumulatedInInvestments" id="idra_AvailableForSaleSecuritiesGrossUnrealizedGainsAccumulatedInInvestments" type="xbrli:monetaryItemType" abstract="false" xbrli:periodType="instant" xbrli:balance="debit" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="AvailableForSaleSecuritiesGrossUnrealizedLossAccumulatedInInvestments" id="idra_AvailableForSaleSecuritiesGrossUnrealizedLossAccumulatedInInvestments" type="xbrli:monetaryItemType" abstract="false" xbrli:periodType="instant" xbrli:balance="credit" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="BusinessCombinationIncreaseDecreaseToReflectLiabilitiesAcquiredAtFairValueAbstract" id="idra_BusinessCombinationIncreaseDecreaseToReflectLiabilitiesAcquiredAtFairValueAbstract" type="xbrli:stringItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="ClassOfWarrantOrRightPeriodOfNoticePriorToRedemption" id="idra_ClassOfWarrantOrRightPeriodOfNoticePriorToRedemption" type="xbrli:durationItemType" abstract="false" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="ClassOfWarrantOrRightRedemptionPricePerShareOfWarrantsOrRights" id="idra_ClassOfWarrantOrRightRedemptionPricePerShareOfWarrantsOrRights" type="us-types:perUnitItemType" abstract="false" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="CommercialPaperDueInOneYearOrLessMember" id="idra_CommercialPaperDueInOneYearOrLessMember" type="nonnum:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="CommitmentContingencyAndRelatedPartyTransactionsAbstract" id="idra_CommitmentContingencyAndRelatedPartyTransactionsAbstract" type="xbrli:stringItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="CommonStockAndWarrantsMember" id="idra_CommonStockAndWarrantsMember" type="nonnum:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="CommonStockIssuedInLieuOfBoardFees" id="idra_CommonStockIssuedInLieuOfBoardFees" type="xbrli:sharesItemType" abstract="false" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="CommonStockWarrantAndOptionExercisesAndEmployeeStockPurchasesMember" id="idra_CommonStockWarrantAndOptionExercisesAndEmployeeStockPurchasesMember" type="nonnum:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="CommonStockWarrantAndOptionExercisesAndEmployeeStockPurchasesTextBlock" id="idra_CommonStockWarrantAndOptionExercisesAndEmployeeStockPurchasesTextBlock" type="nonnum:textBlockItemType" abstract="false" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="CorporateBondsDueInOneYearOrLessMember" id="idra_CorporateBondsDueInOneYearOrLessMember" type="nonnum:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="CorporateBondsDueInOneYearOrMoreMember" id="idra_CorporateBondsDueInOneYearOrMoreMember" type="nonnum:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="DocumentAndEntityInformationAbstract" id="idra_DocumentAndEntityInformationAbstract" type="xbrli:stringItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="EmployeesMember" id="idra_EmployeesMember" type="nonnum:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="EmployeeStockOptionAndWarrantExercisesAndEmployeeStockPurchasePlanPurchasesLineItems" id="idra_EmployeeStockOptionAndWarrantExercisesAndEmployeeStockPurchasePlanPurchasesLineItems" type="xbrli:stringItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="EmployeeStockOptionAndWarrantExercisesAndEmployeeStockPurchasePlanPurchasesTable" id="idra_EmployeeStockOptionAndWarrantExercisesAndEmployeeStockPurchasePlanPurchasesTable" type="xbrli:stringItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrldt:hypercubeItem"/>
  <element name="EquityLineItems" id="idra_EquityLineItems" type="xbrli:stringItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="EstimatedNetProceedsFromIssuanceOfCommonStockAndWarrants" id="idra_EstimatedNetProceedsFromIssuanceOfCommonStockAndWarrants" type="xbrli:monetaryItemType" abstract="false" xbrli:periodType="duration" xbrli:balance="debit" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="ExpectedAgreementTerm" id="idra_ExpectedAgreementTerm" type="xbrli:durationItemType" abstract="false" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="GrossProceedsFromIssuanceOfCommonStockAndWarrants" id="idra_GrossProceedsFromIssuanceOfCommonStockAndWarrants" type="xbrli:monetaryItemType" abstract="false" xbrli:periodType="duration" xbrli:balance="debit" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="LaboratoryEquipmentAndOtherFixedAssetsGross" id="idra_LaboratoryEquipmentAndOtherFixedAssetsGross" type="xbrli:monetaryItemType" abstract="false" xbrli:periodType="instant" xbrli:balance="debit" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="LongTermInvestmentsCorporateNotesAndBondsMember" id="idra_LongTermInvestmentsCorporateNotesAndBondsMember" type="nonnum:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="LongTermInvestmentsMember" id="idra_LongTermInvestmentsMember" type="nonnum:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="LossOnExtinguishmentOfConvertiblePreferredStock" id="idra_LossOnExtinguishmentOfConvertiblePreferredStock" type="xbrli:monetaryItemType" abstract="false" xbrli:periodType="duration" xbrli:balance="debit" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="MaximumAmountThatMayBeCreditedTowardsAnyAmountsDueFromCollaboratorForThirdPartyLicenseIncomeReceived" id="idra_MaximumAmountThatMayBeCreditedTowardsAnyAmountsDueFromCollaboratorForThirdPartyLicenseIncomeReceived" type="xbrli:monetaryItemType" abstract="false" xbrli:periodType="duration" xbrli:balance="debit" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="MaximumPeriodToMaturity" id="idra_MaximumPeriodToMaturity" type="xbrli:durationItemType" abstract="false" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="MaximumTradingDaysConsideredToRedeemWarrants" id="idra_MaximumTradingDaysConsideredToRedeemWarrants" type="xbrli:durationItemType" abstract="false" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="MinimumClosingPriceToRedeemWarrants" id="idra_MinimumClosingPriceToRedeemWarrants" type="us-types:perUnitItemType" abstract="false" xbrli:periodType="instant" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="MinimumTradingDaysConsideredToRedeemWarrants" id="idra_MinimumTradingDaysConsideredToRedeemWarrants" type="xbrli:durationItemType" abstract="false" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="NetProceedsFromIssuanceOfCommonStockAndWarrants" id="idra_NetProceedsFromIssuanceOfCommonStockAndWarrants" type="xbrli:monetaryItemType" abstract="false" xbrli:periodType="duration" xbrli:balance="debit" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="NumberOfSharesOfCommonStockIssuedForStockWarrantAndStockOptionsExercisedAndEsppPurchases" id="idra_NumberOfSharesOfCommonStockIssuedForStockWarrantAndStockOptionsExercisedAndEsppPurchases" type="xbrli:sharesItemType" abstract="false" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="NumberOfSharesOfStockSoldInFinancing" id="idra_NumberOfSharesOfStockSoldInFinancing" type="xbrli:sharesItemType" abstract="false" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="PaymentsOfDividendsPreferredStock" id="idra_PaymentsOfDividendsPreferredStock" type="xbrli:monetaryItemType" abstract="false" xbrli:periodType="duration" xbrli:balance="credit" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="PaymentsPursuantToCompanionDiagnosticAgreement" id="idra_PaymentsPursuantToCompanionDiagnosticAgreement" type="xbrli:monetaryItemType" abstract="false" xbrli:periodType="duration" xbrli:balance="credit" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="PercentageOfThirdPartyLicenseIncomeReceivedCreditedTowardsAnyAmountsDueFromCollaborator" id="idra_PercentageOfThirdPartyLicenseIncomeReceivedCreditedTowardsAnyAmountsDueFromCollaborator" type="num:percentItemType" abstract="false" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="PreferredStockConversionDate" id="idra_PreferredStockConversionDate" type="xbrli:dateItemType" abstract="false" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="PreferredStockSharesDesignated" id="idra_PreferredStockSharesDesignated" type="xbrli:sharesItemType" abstract="false" xbrli:periodType="instant" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="PrefundedWarrantExpirationDate" id="idra_PrefundedWarrantExpirationDate" type="xbrli:dateItemType" abstract="false" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="PrefundedWarrantsAndWarrantsTwoMember" id="idra_PrefundedWarrantsAndWarrantsTwoMember" type="nonnum:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="PrefundedWarrantsMember" id="idra_PrefundedWarrantsMember" type="nonnum:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="PricePerShareOfCommonStock" id="idra_PricePerShareOfCommonStock" type="num:perShareItemType" abstract="false" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="ProceedsFromSaleOfCommonStockAndWarrantsNetOfIssuanceCosts" id="idra_ProceedsFromSaleOfCommonStockAndWarrantsNetOfIssuanceCosts" type="xbrli:monetaryItemType" abstract="false" xbrli:periodType="duration" xbrli:balance="debit" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="ProceedsFromStockIssuedForWarrantAndOptionExercisesAndEsppPurchases" id="idra_ProceedsFromStockIssuedForWarrantAndOptionExercisesAndEsppPurchases" type="xbrli:monetaryItemType" abstract="false" xbrli:periodType="duration" xbrli:balance="debit" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="RestrictedCashAbstract" id="idra_RestrictedCashAbstract" type="xbrli:stringItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="SaleOfCommonAndPreferredStockAndWarrantsTextBlock" id="idra_SaleOfCommonAndPreferredStockAndWarrantsTextBlock" type="nonnum:textBlockItemType" abstract="false" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="SalePricePerShareOfPrefundedWarrants" id="idra_SalePricePerShareOfPrefundedWarrants" type="num:perShareItemType" abstract="false" xbrli:periodType="instant" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="ScheduleOfCommonStockAndWarrantsSoldInMayTwoZeroOneThreeFinancingTableTextBlock" id="idra_ScheduleOfCommonStockAndWarrantsSoldInMayTwoZeroOneThreeFinancingTableTextBlock" type="nonnum:textBlockItemType" abstract="false" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="ScheduleOfEquityTable" id="idra_ScheduleOfEquityTable" type="xbrli:stringItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrldt:hypercubeItem"/>
  <element name="ScheduleOfOtherRelatedPartyTransactionsLineItems" id="idra_ScheduleOfOtherRelatedPartyTransactionsLineItems" type="xbrli:stringItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="SeriesDAndEPreferredStockMember" id="idra_SeriesDAndEPreferredStockMember" type="nonnum:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="ShortTermInvestmentsCommercialPaperMember" id="idra_ShortTermInvestmentsCommercialPaperMember" type="nonnum:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="ShortTermInvestmentsCorporateNotesAndBondsMember" id="idra_ShortTermInvestmentsCorporateNotesAndBondsMember" type="nonnum:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="TermOfWarrants" id="idra_TermOfWarrants" type="xbrli:durationItemType" abstract="false" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item"/>
  <element name="WarrantsMatchingMember" id="idra_WarrantsMatchingMember" type="nonnum:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item"/>
</schema>


