<?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>

