<ownershipDocument>
    <schemaVersion>X0201</schemaVersion>

    <documentType>4</documentType>
<periodOfReport>2003-12-02</periodOfReport>
<notSubjectToSection16>0</notSubjectToSection16>
    <issuer>
        <issuerCik>0000913077</issuerCik>
        <issuerName>AFFYMETRIX INC</issuerName>
        <issuerTradingSymbol>AFFX</issuerTradingSymbol>
</issuer>
<reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001240366</rptOwnerCik>
            <rptOwnerName>SINGER DAVID B</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O AFFYMETRIX, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>3380 CENTRAL EXPRESSWAY</rptOwnerStreet2>
            <rptOwnerCity>SANTA CLARA</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>95051</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
            <reportingOwnerRelationship>
<isDirector>1</isDirector>
<isOfficer>0</isOfficer>
<isTenPercentOwner>0</isTenPercentOwner>
<isOther>0</isOther>
<officerTitle></officerTitle>
<otherText></otherText>
</reportingOwnerRelationship>
</reportingOwner>
<nonDerivativeTable><nonDerivativeTransaction><securityTitle><value>Common Stock</value>
</securityTitle>
<transactionDate><value>2003-12-02</value>
</transactionDate>
<transactionCoding><transactionFormType>4</transactionFormType>
<transactionCode>M</transactionCode>
<equitySwapInvolved>0</equitySwapInvolved>
</transactionCoding>
<transactionAmounts><transactionShares><value>500</value>
</transactionShares>
<transactionPricePerShare><value>.3375</value>
</transactionPricePerShare>
<transactionAcquiredDisposedCode><value>A</value>
</transactionAcquiredDisposedCode>
</transactionAmounts>
<postTransactionAmounts><sharesOwnedFollowingTransaction><value>0</value>
</sharesOwnedFollowingTransaction>
</postTransactionAmounts>
<ownershipNature><directOrIndirectOwnership><value>D</value>
</directOrIndirectOwnership>
</ownershipNature>
</nonDerivativeTransaction>
<nonDerivativeTransaction><securityTitle><value>Common Stock</value>
</securityTitle>
<transactionDate><value>2003-12-02</value>
</transactionDate>
<transactionCoding><transactionFormType>4</transactionFormType>
<transactionCode>S</transactionCode>
<equitySwapInvolved>0</equitySwapInvolved>
</transactionCoding>
<transactionAmounts><transactionShares><value>500</value>
<footnoteId id="F1"></footnoteId>
</transactionShares>
<transactionPricePerShare><value>25.76</value>
</transactionPricePerShare>
<transactionAcquiredDisposedCode><value>D</value>
</transactionAcquiredDisposedCode>
</transactionAmounts>
<postTransactionAmounts><sharesOwnedFollowingTransaction><value>26332</value>
</sharesOwnedFollowingTransaction>
</postTransactionAmounts>
<ownershipNature><directOrIndirectOwnership><value>D</value>
</directOrIndirectOwnership>
</ownershipNature>
</nonDerivativeTransaction>
<nonDerivativeHolding><securityTitle><value>Common Stock</value>
</securityTitle>
<postTransactionAmounts><sharesOwnedFollowingTransaction><value>2000</value>
</sharesOwnedFollowingTransaction>
</postTransactionAmounts>
<ownershipNature><directOrIndirectOwnership><value>I</value>
</directOrIndirectOwnership>
<natureOfOwnership><value>Chevy Chase Circle Foundation</value>
<footnoteId id="F2"></footnoteId>
</natureOfOwnership>
</ownershipNature>
</nonDerivativeHolding>
</nonDerivativeTable>
<derivativeTable><derivativeTransaction><securityTitle><value>Options to Purchase Common Stock</value>
</securityTitle>
<conversionOrExercisePrice><value>.3375</value>
</conversionOrExercisePrice>
<transactionDate><value>2003-12-02</value>
</transactionDate>
<transactionCoding><transactionFormType>4</transactionFormType>
<transactionCode>M</transactionCode>
<equitySwapInvolved>0</equitySwapInvolved>
</transactionCoding>
<transactionAmounts><transactionShares><value>500</value>
</transactionShares>
<transactionPricePerShare><value>0</value>
</transactionPricePerShare>
<transactionAcquiredDisposedCode><value>D</value>
</transactionAcquiredDisposedCode>
</transactionAmounts>
<exerciseDate><footnoteId id="F3"></footnoteId>
</exerciseDate>
<expirationDate><value>2005-12-20</value>
</expirationDate>
<underlyingSecurity><underlyingSecurityTitle><value>Common Stock</value>
</underlyingSecurityTitle>
<underlyingSecurityShares><value>500</value>
</underlyingSecurityShares>
</underlyingSecurity>
<postTransactionAmounts><sharesOwnedFollowingTransaction><value>39666</value>
</sharesOwnedFollowingTransaction>
</postTransactionAmounts>
<ownershipNature><directOrIndirectOwnership><value>D</value>
</directOrIndirectOwnership>
</ownershipNature>
</derivativeTransaction>
</derivativeTable>
<footnotes><footnote id="F1">Sold pursuant to a 10b5-1 Sales Plan entered into on August 8, 2003 by the reporting person.</footnote>
<footnote id="F2">Held by Chevy Chase Circle Foundation which is controlled by the reporting person.</footnote>
<footnote id="F3">13,334 shares exercisable on 12/20/96 and 13,333 shares exercisable on each of the following: 12/20/97, 12/20/98, 12/20/99 and 12/20/00.</footnote>
</footnotes>
<ownerSignature><signatureName>/s/ David B. Singer</signatureName>
<signatureDate>2003-12-04</signatureDate>
</ownerSignature>
</ownershipDocument>

