<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0202</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2006-01-31</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001002637</issuerCik>
        <issuerName>MILLENNIUM PHARMACEUTICALS INC</issuerName>
        <issuerTradingSymbol>MLNM</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001347582</rptOwnerCik>
            <rptOwnerName>Protopapas Anna</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>MILLENNIUM PHARMACEUTICALS, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>40 LANDSDOWNE STREET</rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02139</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>Senior Vice President</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Employee stock option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>8.38</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <value>2015-05-31</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>8333</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Became exercisable for 2/48ths of the total number of shares granted on 05/31/2005 and for 1/48th of the total number of shares granted monthly thereafter beginning 06/01/2005.</footnote>
    </footnotes>

    <remarks>This is the second of two Forms 3 filed by the reporting person on the same date.  This continues the information provided in Table II of the first Form 3 filed on this date.</remarks>

    <ownerSignature>
        <signatureName>Jean L. Ernst, Attorney-In-Fact</signatureName>
        <signatureDate>2006-02-08</signatureDate>
    </ownerSignature>
</ownershipDocument>
