<?xml version="1.0"?>
<ownershipDocument>
    <schemaVersion>X0201</schemaVersion>

    <documentType>4</documentType><periodOfReport>2003-12-10</periodOfReport>
    <issuer>
        <issuerCik>0001002637</issuerCik>
        <issuerName>MILLENNIUM PHARMACEUTICALS INC</issuerName>
        <issuerTradingSymbol>MLNM</issuerTradingSymbol></issuer><reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001192613</rptOwnerCik>
            <rptOwnerName>SELBY NORMAN C</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>TRANSFORM PHARMACEUTICALS, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>29 HARTWELL AVENUE</rptOwnerStreet2>
            <rptOwnerCity>LEXINGTON,</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02421</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
            <reportingOwnerRelationship>
<isDirector>1</isDirector><isOfficer>0</isOfficer><isTenPercentOwner>0</isTenPercentOwner><isOther>0</isOther></reportingOwnerRelationship></reportingOwner><nonDerivativeTable><nonDerivativeTransaction><securityTitle><value>Common stock</value></securityTitle><transactionDate><value>2003-12-10</value></transactionDate><transactionCoding><transactionFormType>5</transactionFormType><transactionCode>G</transactionCode><equitySwapInvolved>0</equitySwapInvolved><footnoteId id="F1"/></transactionCoding><transactionAmounts><transactionShares><value>1010</value></transactionShares><transactionPricePerShare><value>0</value></transactionPricePerShare><transactionAcquiredDisposedCode><value>D</value></transactionAcquiredDisposedCode></transactionAmounts><postTransactionAmounts><sharesOwnedFollowingTransaction><value>8010</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership><natureOfOwnership><value/></natureOfOwnership></ownershipNature></nonDerivativeTransaction><nonDerivativeTransaction><securityTitle><value>Common stock</value></securityTitle><transactionDate><value>2003-12-10</value></transactionDate><transactionCoding><transactionFormType>5</transactionFormType><transactionCode>G</transactionCode><equitySwapInvolved>0</equitySwapInvolved><footnoteId id="F2"/></transactionCoding><transactionAmounts><transactionShares><value>1010</value></transactionShares><transactionPricePerShare><value>0</value></transactionPricePerShare><transactionAcquiredDisposedCode><value>D</value></transactionAcquiredDisposedCode></transactionAmounts><postTransactionAmounts><sharesOwnedFollowingTransaction><value>7000</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership><natureOfOwnership><value/></natureOfOwnership></ownershipNature></nonDerivativeTransaction><nonDerivativeTransaction><securityTitle><value>Common stock</value></securityTitle><transactionDate><value>2003-12-10</value></transactionDate><transactionCoding><transactionFormType>5</transactionFormType><transactionCode>G</transactionCode><equitySwapInvolved>0</equitySwapInvolved><footnoteId id="F1"/></transactionCoding><transactionAmounts><transactionShares><value>1010</value></transactionShares><transactionPricePerShare><value>0</value></transactionPricePerShare><transactionAcquiredDisposedCode><value>A</value></transactionAcquiredDisposedCode></transactionAmounts><postTransactionAmounts><sharesOwnedFollowingTransaction><value>1010</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>I</value></directOrIndirectOwnership><natureOfOwnership><value>by trust for son</value></natureOfOwnership></ownershipNature></nonDerivativeTransaction><nonDerivativeTransaction><securityTitle><value>Common stock</value></securityTitle><transactionDate><value>2003-12-10</value></transactionDate><transactionCoding><transactionFormType>5</transactionFormType><transactionCode>G</transactionCode><equitySwapInvolved>0</equitySwapInvolved><footnoteId id="F2"/></transactionCoding><transactionAmounts><transactionShares><value>1010</value></transactionShares><transactionPricePerShare><value>0</value></transactionPricePerShare><transactionAcquiredDisposedCode><value>A</value></transactionAcquiredDisposedCode></transactionAmounts><postTransactionAmounts><sharesOwnedFollowingTransaction><value>1010</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>I</value></directOrIndirectOwnership><natureOfOwnership><value>by trust for son</value></natureOfOwnership></ownershipNature></nonDerivativeTransaction><nonDerivativeHolding><securityTitle><value>Common stock</value></securityTitle><postTransactionAmounts><sharesOwnedFollowingTransaction><value>7000</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership><natureOfOwnership><value/></natureOfOwnership></ownershipNature></nonDerivativeHolding><nonDerivativeHolding><securityTitle><value>Common stock</value></securityTitle><postTransactionAmounts><sharesOwnedFollowingTransaction><value>1010</value><footnoteId id="F3"/></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>I</value></directOrIndirectOwnership><natureOfOwnership><value>by trust for son</value></natureOfOwnership></ownershipNature></nonDerivativeHolding><nonDerivativeHolding><securityTitle><value>Common stock</value></securityTitle><postTransactionAmounts><sharesOwnedFollowingTransaction><value>1010</value><footnoteId id="F4"/></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>I</value></directOrIndirectOwnership><natureOfOwnership><value>by trust for son</value></natureOfOwnership></ownershipNature></nonDerivativeHolding></nonDerivativeTable><footnotes><footnote id="F1">Transfer of 1,010 shares to the Luke Vail Selby Trust</footnote><footnote id="F2">Transfer of 1,010 shares to the Thomas Vail Selby Trust</footnote><footnote id="F3">Held by the Luke Vail Selby Trust.  Mr. Selby disclaims beneficial ownership of these shares.</footnote><footnote id="F4">Held by the Thomas Vail Selby Trust.  Mr. Selby disclaims beneficial ownership of these shares.</footnote></footnotes><remarks/><ownerSignature><signatureName>Joel S. Goldberg, Attorney-In-Fact</signatureName><signatureDate>2003-12-11</signatureDate></ownerSignature></ownershipDocument>

