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Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
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MIC-Info: RSA-MD5,RSA,
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<SEC-DOCUMENT>0001104659-03-015360.txt : 20030820
<SEC-HEADER>0001104659-03-015360.hdr.sgml : 20030820
<ACCEPTANCE-DATETIME>20030722122017
ACCESSION NUMBER:		0001104659-03-015360
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20030717
FILED AS OF DATE:		20030721
DATE AS OF CHANGE:		20030820

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:		3380 CENTRAL EXPRESSWAY
		CITY:			SANTA CLARA
		STATE:			CA
		ZIP:			95051
		BUSINESS PHONE:		4085226000

	MAIL ADDRESS:	
		STREET 1:		3380 CENTRAL EXPRESSWAY
		CITY:			SANTA CLARA
		STATE:			CA
		ZIP:			95051

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			BERG PAUL
		CENTRAL INDEX KEY:			0001198229

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-28218
		FILM NUMBER:		03795931

	BUSINESS ADDRESS:	
		STREET 1:		STANFORD UNIVERSITY SCHOOL OF MEDICINE
		STREET 2:		BECKMAN CENTER #B062
		CITY:			STANFORD
		STATE:			CA
		ZIP:			94305
		BUSINESS PHONE:		6507236170

	MAIL ADDRESS:	
		STREET 1:		STANFORD UNIVERSITY SCHOOL OF MEDICINE
		STREET 2:		#B062
		CITY:			STANFORD
		STATE:			CA
		ZIP:			94305
</SEC-HEADER>
<DOCUMENT>
<TYPE>4
<SEQUENCE>1
<FILENAME>a4.xml
<DESCRIPTION>4
<TEXT>
<XML>
<?xml version="1.0" encoding="utf-8"?>
<ownershipDocument>
    <schemaVersion>X0101</schemaVersion>

    <documentType>4</documentType>
  <periodOfReport>2003-07-17</periodOfReport>
  <notSubjectToSection16>0</notSubjectToSection16>
    <issuer>
        <issuerCik>0000913077</issuerCik>
        <issuerName>AFFYMETRIX INC</issuerName>
        <issuerTradingSymbol>AFFX</issuerTradingSymbol>
  </issuer>
  <reportingOwner>
    <reportingOwnerId>
            <rptOwnerCik>0001198229</rptOwnerCik>
            <rptOwnerName>BERG PAUL</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>  </rptOwnerStreet1>
            <rptOwnerStreet2>  </rptOwnerStreet2>
            <rptOwnerCity>  </rptOwnerCity>
            <rptOwnerState>  </rptOwnerState>
            <rptOwnerZipCode>  </rptOwnerZipCode>
        </reportingOwnerAddress>
            <reportingOwnerRelationship>
      <isDirector>1</isDirector>
      <isOfficer>0</isOfficer>
      <isTenPercentOwner>0</isTenPercentOwner>
      <isOther>0</isOther>
    </reportingOwnerRelationship>
  </reportingOwner>
  <derivativeSecurity>
    <securityTitle>
      <value>Options to Purchase Common Stock</value>
      <footnoteId id="F1"/>
    </securityTitle>
    <conversionOrExercisePrice>
      <value>21.17</value>
    </conversionOrExercisePrice>
    <transactionDate>
      <value>2003-07-17</value>
    </transactionDate>
    <transactionCoding>
      <transactionFormType>4</transactionFormType>
      <transactionCode>A</transactionCode>
      <equitySwapInvolved>0</equitySwapInvolved>
    </transactionCoding>
    <transactionTimeliness>
      <value/>
    </transactionTimeliness>
    <transactionAmounts>
      <transactionShares>
        <value>10000</value>
      </transactionShares>
      <transactionValue>
        <value>0</value>
      </transactionValue>
      <transactionAcquiredDisposedCode>
        <value>A</value>
      </transactionAcquiredDisposedCode>
    </transactionAmounts>
    <exerciseDate>
      <value>2004-07-17</value>
    </exerciseDate>
    <expirationDate>
      <value>2013-07-19</value>
    </expirationDate>
    <underlyingSecurity>
      <underlyingSecurityTitle>
        <value>Common stock</value>
      </underlyingSecurityTitle>
      <underlyingSecurityShares>
        <value>10000</value>
      </underlyingSecurityShares>
    </underlyingSecurity>
    <postTransactionAmounts>
      <sharesOwnedFollowingTransaction>
        <value>10000</value>
      </sharesOwnedFollowingTransaction>
    </postTransactionAmounts>
    <ownershipNature>
      <directOrIndirectOwnership>
        <value>D</value>
      </directOrIndirectOwnership>
    </ownershipNature>
  </derivativeSecurity>
  <footnotes>
    <footnote id="F1">Granted pursuant to the provisions set forth in the Amended and Restated 1996 Nonemployee Directors Stock Option Plan of Affymetrix, Inc.</footnote>
  </footnotes>
  <ownerSignature>
    <signatureName>/s/ Paul Berg</signatureName>
    <signatureDate>2003-07-21</signatureDate>
  </ownerSignature>
</ownershipDocument>

</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
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