<?xml version="1.0" encoding="utf-8"?>
<ownershipDocument>
    <schemaVersion>X0201</schemaVersion>

    <documentType>4</documentType>
  <periodOfReport>2003-09-16</periodOfReport>
  <notSubjectToSection16>0</notSubjectToSection16>
    <issuer>
        <issuerCik>0000820237</issuerCik>
        <issuerName>GEN PROBE INC</issuerName>
        <issuerTradingSymbol>GPRO</issuerTradingSymbol>
  </issuer>
  <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001230054</rptOwnerCik>
            <rptOwnerName>NORDHOFF HENRY L</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>GEN-PROBE INCORPORATED</rptOwnerStreet1>
            <rptOwnerStreet2>10210 GENETIC CENTER DRIVE</rptOwnerStreet2>
            <rptOwnerCity>SAN DIEGO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>92121</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
            <reportingOwnerRelationship>
      <isDirector>1</isDirector>
      <isOfficer>1</isOfficer>
      <isTenPercentOwner>0</isTenPercentOwner>
      <isOther>0</isOther>
      <officerTitle>CEO and President</officerTitle>
    </reportingOwnerRelationship>
  </reportingOwner>
  <nonDerivativeTable>
    <nonDerivativeTransaction>
      <securityTitle>
        <value>Common Stock</value>
      </securityTitle>
      <transactionDate>
        <value>2003-09-16</value>
      </transactionDate>
      <transactionCoding>
        <transactionFormType>4</transactionFormType>
        <transactionCode>M</transactionCode>
        <equitySwapInvolved>0</equitySwapInvolved>
      </transactionCoding>
      <transactionTimeliness>
        <value></value>
      </transactionTimeliness>
      <transactionAmounts>
        <transactionShares>
          <value>26541</value>
        </transactionShares>
        <transactionPricePerShare>
          <value>24.58</value>
        </transactionPricePerShare>
        <transactionAcquiredDisposedCode>
          <value>A</value>
        </transactionAcquiredDisposedCode>
      </transactionAmounts>
      <postTransactionAmounts>
        <sharesOwnedFollowingTransaction>
          <value>40627</value>
        </sharesOwnedFollowingTransaction>
      </postTransactionAmounts>
      <ownershipNature>
        <directOrIndirectOwnership>
          <value>D</value>
        </directOrIndirectOwnership>
      </ownershipNature>
    </nonDerivativeTransaction>
    <nonDerivativeTransaction>
      <securityTitle>
        <value>Common Stock</value>
      </securityTitle>
      <transactionDate>
        <value>2003-09-16</value>
      </transactionDate>
      <transactionCoding>
        <transactionFormType>4</transactionFormType>
        <transactionCode>M</transactionCode>
        <equitySwapInvolved>0</equitySwapInvolved>
      </transactionCoding>
      <transactionTimeliness>
        <value></value>
      </transactionTimeliness>
      <transactionAmounts>
        <transactionShares>
          <value>20459</value>
        </transactionShares>
        <transactionPricePerShare>
          <value>24.58</value>
        </transactionPricePerShare>
        <transactionAcquiredDisposedCode>
          <value>A</value>
        </transactionAcquiredDisposedCode>
      </transactionAmounts>
      <postTransactionAmounts>
        <sharesOwnedFollowingTransaction>
          <value>61086</value>
        </sharesOwnedFollowingTransaction>
      </postTransactionAmounts>
      <ownershipNature>
        <directOrIndirectOwnership>
          <value>D</value>
        </directOrIndirectOwnership>
      </ownershipNature>
    </nonDerivativeTransaction>
    <nonDerivativeTransaction>
      <securityTitle>
        <value>Common Stock</value>
      </securityTitle>
      <transactionDate>
        <value>2003-09-16</value>
      </transactionDate>
      <transactionCoding>
        <transactionFormType>4</transactionFormType>
        <transactionCode>S</transactionCode>
        <equitySwapInvolved>0</equitySwapInvolved>
        <footnoteId id="F1"/>
      </transactionCoding>
      <transactionTimeliness>
        <value></value>
      </transactionTimeliness>
      <transactionAmounts>
        <transactionShares>
          <value>47000</value>
        </transactionShares>
        <transactionPricePerShare>
          <value>57.3623</value>
        </transactionPricePerShare>
        <transactionAcquiredDisposedCode>
          <value>D</value>
        </transactionAcquiredDisposedCode>
      </transactionAmounts>
      <postTransactionAmounts>
        <sharesOwnedFollowingTransaction>
          <value>4086</value>
        </sharesOwnedFollowingTransaction>
      </postTransactionAmounts>
      <ownershipNature>
        <directOrIndirectOwnership>
          <value>D</value>
        </directOrIndirectOwnership>
      </ownershipNature>
    </nonDerivativeTransaction>
  </nonDerivativeTable>
  <derivativeTable>
    <derivativeTransaction>
      <securityTitle>
        <value>Employee Stock Option (Right to Buy)</value>
      </securityTitle>
      <conversionOrExercisePrice>
        <value>24.58</value>
      </conversionOrExercisePrice>
      <transactionDate>
        <value>2003-09-16</value>
      </transactionDate>
      <transactionCoding>
        <transactionFormType>4</transactionFormType>
        <transactionCode>M</transactionCode>
        <equitySwapInvolved>0</equitySwapInvolved>
      </transactionCoding>
      <transactionTimeliness>
        <value></value>
      </transactionTimeliness>
      <transactionAmounts>
        <transactionShares>
          <value>26541</value>
        </transactionShares>
        <transactionPricePerShare>
          <value>0</value>
        </transactionPricePerShare>
        <transactionAcquiredDisposedCode>
          <value>D</value>
        </transactionAcquiredDisposedCode>
      </transactionAmounts>
      <exerciseDate>
        <footnoteId id="F2"/>
      </exerciseDate>
      <expirationDate>
        <value>2011-09-01</value>
      </expirationDate>
      <underlyingSecurity>
        <underlyingSecurityTitle>
          <value>Common Stock</value>
        </underlyingSecurityTitle>
        <underlyingSecurityShares>
          <value>26541</value>
        </underlyingSecurityShares>
      </underlyingSecurity>
      <postTransactionAmounts>
        <sharesOwnedFollowingTransaction>
          <value>3948</value>
        </sharesOwnedFollowingTransaction>
      </postTransactionAmounts>
      <ownershipNature>
        <directOrIndirectOwnership>
          <value>D</value>
        </directOrIndirectOwnership>
      </ownershipNature>
    </derivativeTransaction>
    <derivativeTransaction>
      <securityTitle>
        <value>Employee Stock Option (Right to Buy)</value>
      </securityTitle>
      <conversionOrExercisePrice>
        <value>24.58</value>
      </conversionOrExercisePrice>
      <transactionDate>
        <value>2003-09-16</value>
      </transactionDate>
      <transactionCoding>
        <transactionFormType>4</transactionFormType>
        <transactionCode>M</transactionCode>
        <equitySwapInvolved>0</equitySwapInvolved>
      </transactionCoding>
      <transactionTimeliness>
        <value></value>
      </transactionTimeliness>
      <transactionAmounts>
        <transactionShares>
          <value>20459</value>
        </transactionShares>
        <transactionPricePerShare>
          <value>0</value>
        </transactionPricePerShare>
        <transactionAcquiredDisposedCode>
          <value>D</value>
        </transactionAcquiredDisposedCode>
      </transactionAmounts>
      <exerciseDate>
        <footnoteId id="F3"/>
      </exerciseDate>
      <expirationDate>
        <value>2012-06-01</value>
      </expirationDate>
      <underlyingSecurity>
        <underlyingSecurityTitle>
          <value>Common Stock</value>
        </underlyingSecurityTitle>
        <underlyingSecurityShares>
          <value>20459</value>
        </underlyingSecurityShares>
      </underlyingSecurity>
      <postTransactionAmounts>
        <sharesOwnedFollowingTransaction>
          <value>260829</value>
        </sharesOwnedFollowingTransaction>
      </postTransactionAmounts>
      <ownershipNature>
        <directOrIndirectOwnership>
          <value>D</value>
        </directOrIndirectOwnership>
      </ownershipNature>
    </derivativeTransaction>
  </derivativeTable>
  <footnotes>
    <footnote id="F1">The sales reported in this Form 4 were effected pursuant to a Rule 10b-5-1 trading plan adopted by the reporting person on September 15,  2003.</footnote>
    <footnote id="F2">Option vests as follows: 25% on 9/1/02; 1/48th vesting monthly thereafter following three years.</footnote>
    <footnote id="F3">Option vests as follows: 25% on 6/1/03; 1/48th vesting monthly thereafter following three years.</footnote>
  </footnotes>
  <ownerSignature>
    <signatureName>/s/ R. William Bowen, Attorney-in-Fact</signatureName>
    <signatureDate>2003-09-18</signatureDate>
  </ownerSignature>
</ownershipDocument>

