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Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
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 TWSM7vrzLADbmYQaionwg5sDW3P6oaM5D3tdezXMm7z1T+B+twIDAQAB
MIC-Info: RSA-MD5,RSA,
 B8QmUL7x+6c+13VPZavN02gtavZL9pJy4eK3De2lW74r1YR+jCxlJ3KYklhy851x
 FfEvYXB+Q4qXcac2nqQWWQ==

<SEC-DOCUMENT>0001179110-09-002286.txt : 20090209
<SEC-HEADER>0001179110-09-002286.hdr.sgml : 20090209
<ACCEPTANCE-DATETIME>20090209161358
ACCESSION NUMBER:		0001179110-09-002286
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20090205
FILED AS OF DATE:		20090209
DATE AS OF CHANGE:		20090209

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			BATTY JOHN
		CENTRAL INDEX KEY:			0001143936

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-28218
		FILM NUMBER:		09581453

	BUSINESS ADDRESS:	
		STREET 1:		6900 PASEO PADRE PARKWAY
		CITY:			FREMONT
		STATE:			CA
		ZIP:			94555
		BUSINESS PHONE:		5107137300

ISSUER:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			AFFYMETRIX INC
		CENTRAL INDEX KEY:			0000913077
		STANDARD INDUSTRIAL CLASSIFICATION:	LABORATORY ANALYTICAL INSTRUMENTS [3826]
		IRS NUMBER:				770319159
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			1231

	BUSINESS ADDRESS:	
		STREET 1:		3420 CENTRAL EXPRESSWAY
		CITY:			SANTA CLARA
		STATE:			CA
		ZIP:			95051
		BUSINESS PHONE:		4087315000

	MAIL ADDRESS:	
		STREET 1:		3420 CENTRAL EXPRESSWAY
		CITY:			SANTA CLARA
		STATE:			CA
		ZIP:			95051
</SEC-HEADER>
<DOCUMENT>
<TYPE>4
<SEQUENCE>1
<FILENAME>edgar.xml
<DESCRIPTION>FORM 4 -
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0303</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2009-02-05</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0000913077</issuerCik>
        <issuerName>AFFYMETRIX INC</issuerName>
        <issuerTradingSymbol>AFFX</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001143936</rptOwnerCik>
            <rptOwnerName>BATTY JOHN</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O AFFYMETRIX, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>3420 CENTRAL EXPRESSWAY</rptOwnerStreet2>
            <rptOwnerCity>SANTA CLARA</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>95051</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>Chief Financial Officer</officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2009-02-05</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>F</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>991</value>
                    <footnoteId id="F1"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>3.39</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>48527</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <derivativeTable></derivativeTable>

    <footnotes>
        <footnote id="F1">Represents the number of shares withheld by Affymetrix, Inc. to cover the tax liability resulting from the scheduled vesting of a restricted stock award previously granted.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>/s/ John C. Batty</signatureName>
        <signatureDate>2009-02-06</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
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