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

    <schemaVersion>X0202</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2008-05-14</periodOfReport>

    <notSubjectToSection16>1</notSubjectToSection16>

    <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>PERSEUS, L.L.C.</rptOwnerStreet1>
            <rptOwnerStreet2>1325 AVENUE OF THE AMERICAS</rptOwnerStreet2>
            <rptOwnerCity>NEW YORK</rptOwnerCity>
            <rptOwnerState>NY</rptOwnerState>
            <rptOwnerZipCode>10019</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable></nonDerivativeTable>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Stock option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>19.76</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2008-05-14</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>D</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>2667</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <value>2012-05-01</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>2667</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
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                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
        <derivativeTransaction>
            <securityTitle>
                <value>Director stock option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
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            </conversionOrExercisePrice>
            <transactionDate>
                <value>2008-05-14</value>
            </transactionDate>
            <transactionCoding>
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                <transactionCode>D</transactionCode>
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                </transactionShares>
                <transactionPricePerShare>
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                </transactionPricePerShare>
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            <exerciseDate>
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            <expirationDate>
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            <underlyingSecurity>
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                </underlyingSecurityTitle>
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                </underlyingSecurityShares>
            </underlyingSecurity>
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            </postTransactionAmounts>
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            </ownershipNature>
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        <derivativeTransaction>
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                </transactionShares>
                <transactionPricePerShare>
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                </transactionPricePerShare>
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            <expirationDate>
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                </underlyingSecurityTitle>
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                </underlyingSecurityShares>
            </underlyingSecurity>
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        </derivativeTransaction>
        <derivativeTransaction>
            <securityTitle>
                <value>Stock option (right to buy)</value>
            </securityTitle>
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            </conversionOrExercisePrice>
            <transactionDate>
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            </transactionDate>
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                </transactionShares>
                <transactionPricePerShare>
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            <expirationDate>
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                </underlyingSecurityTitle>
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                </underlyingSecurityShares>
            </underlyingSecurity>
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        </derivativeTransaction>
        <derivativeTransaction>
            <securityTitle>
                <value>Stock option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
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            </conversionOrExercisePrice>
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            </transactionDate>
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            <transactionAmounts>
                <transactionShares>
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                </transactionShares>
                <transactionPricePerShare>
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                <transactionPricePerShare>
                    <value>0</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <value>2017-05-01</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>5000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
        <derivativeTransaction>
            <securityTitle>
                <value>Stock option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>10.87</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2008-05-14</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>D</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>15000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <value>2017-05-31</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>15000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
        <derivativeTransaction>
            <securityTitle>
                <value>Restricted stock units</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F2"/>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2008-05-14</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>D</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>5000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F3"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F3"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>5000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">This option was cancelled in the merger (the &quot;Merger&quot;) of Mahogany Acquisition Corp. with and into Millennium Pharmaceuticals, Inc. (&quot;Millennium&quot;) in exchange for a cash payment per underlying share equal to the difference between the exercise price and $25.00.</footnote>
        <footnote id="F2">Each restricted stock unit represents a contingent right to receive one share of Millennium common stock.</footnote>
        <footnote id="F3">Each restricted stock unit award was cancelled in the Merger in exchange for $25.00 per share of Millennium common stock underlying the restricted stock unit award.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>Joel S. Goldberg, Attorney-In-Fact</signatureName>
        <signatureDate>2008-05-15</signatureDate>
    </ownerSignature>
</ownershipDocument>
