<ownershipDocument>
    <schemaVersion>X0201</schemaVersion>

    <documentType>4</documentType>
<periodOfReport>2003-01-05</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>President &amp; CEO</officerTitle>
<otherText></otherText>
</reportingOwnerRelationship>
</reportingOwner>
<nonDerivativeTable><nonDerivativeTransaction><securityTitle><value>Common Stock</value>
</securityTitle>
<transactionDate><value>2004-01-05</value>
</transactionDate>
<transactionCoding><transactionFormType>4</transactionFormType>
<transactionCode>M</transactionCode>
<equitySwapInvolved>0</equitySwapInvolved>
</transactionCoding>
<transactionAmounts><transactionShares><value>4000</value>
</transactionShares>
<transactionPricePerShare><value>12.29</value>
</transactionPricePerShare>
<transactionAcquiredDisposedCode><value>A</value>
</transactionAcquiredDisposedCode>
</transactionAmounts>
<postTransactionAmounts><sharesOwnedFollowingTransaction><value>8086</value>
</sharesOwnedFollowingTransaction>
</postTransactionAmounts>
<ownershipNature><directOrIndirectOwnership><value>D</value>
</directOrIndirectOwnership>
</ownershipNature>
</nonDerivativeTransaction>
<nonDerivativeTransaction><securityTitle><value>Common Stock</value>
</securityTitle>
<transactionDate><value>2004-01-05</value>
</transactionDate>
<transactionCoding><transactionFormType>4</transactionFormType>
<transactionCode>S</transactionCode>
<equitySwapInvolved>0</equitySwapInvolved>
<footnoteId id="F1"></footnoteId>
</transactionCoding>
<transactionAmounts><transactionShares><value>4000</value>
</transactionShares>
<transactionPricePerShare><value>35.01</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>12.29</value>
</conversionOrExercisePrice>
<transactionDate><value>2004-01-05</value>
</transactionDate>
<transactionCoding><transactionFormType>4</transactionFormType>
<transactionCode>M</transactionCode>
<equitySwapInvolved>0</equitySwapInvolved>
</transactionCoding>
<transactionAmounts><transactionShares><value>4000</value>
</transactionShares>
<transactionPricePerShare><value>0</value>
</transactionPricePerShare>
<transactionAcquiredDisposedCode><value>D</value>
</transactionAcquiredDisposedCode>
</transactionAmounts>
<exerciseDate><footnoteId id="F2"></footnoteId>
</exerciseDate>
<expirationDate><value>2012-06-01</value>
</expirationDate>
<underlyingSecurity><underlyingSecurityTitle><value>Common Stock</value>
</underlyingSecurityTitle>
<underlyingSecurityShares><value>4000</value>
</underlyingSecurityShares>
</underlyingSecurity>
<postTransactionAmounts><sharesOwnedFollowingTransaction><value>480673</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 10b5-1 trading plan adopted by the reporting person on September 15, 2003.</footnote>
<footnote id="F2">Option vests as follows: 25% vest on 6/1/03; 1/48th vesting monthly following three years.</footnote>
</footnotes>
<ownerSignature><signatureName>/s/ R. William Bowen, Attorney-in-Fact</signatureName>
<signatureDate>2004-01-06</signatureDate>
</ownerSignature>
</ownershipDocument>

