<ownershipDocument>
    <schemaVersion>X0201</schemaVersion>

    <documentType>4/A</documentType>
<periodOfReport>2003-10-01</periodOfReport>
<dateOfOriginalSubmission>2003-10-03</dateOfOriginalSubmission>
<notSubjectToSection16>0</notSubjectToSection16>
    <issuer>
        <issuerCik>0000820237</issuerCik>
        <issuerName>GEN PROBE INC</issuerName>
        <issuerTradingSymbol>GPRO</issuerTradingSymbol>
</issuer>
<reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001265721</rptOwnerCik>
            <rptOwnerName>ARNOLD LYLE J</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>0</isDirector>
<isOfficer>1</isOfficer>
<isTenPercentOwner>0</isTenPercentOwner>
<isOther>0</isOther>
<officerTitle>VP, Research</officerTitle>
<otherText></otherText>
</reportingOwnerRelationship>
</reportingOwner>
<nonDerivativeTable></nonDerivativeTable>
<derivativeTable><derivativeTransaction><securityTitle><value>Employee Stock Option (Right to Buy)</value>
</securityTitle>
<conversionOrExercisePrice><value>27.08</value>
</conversionOrExercisePrice>
<transactionDate><value>2003-10-01</value>
<footnoteId id="F1"></footnoteId>
</transactionDate>
<transactionCoding><transactionFormType>4</transactionFormType>
<transactionCode>A</transactionCode>
<equitySwapInvolved>0</equitySwapInvolved>
</transactionCoding>
<transactionAmounts><transactionShares><value>20000</value>
<footnoteId id="F1"></footnoteId>
</transactionShares>
<transactionPricePerShare><value>0</value>
</transactionPricePerShare>
<transactionAcquiredDisposedCode><value>A</value>
</transactionAcquiredDisposedCode>
</transactionAmounts>
<exerciseDate><footnoteId id="F2"></footnoteId>
</exerciseDate>
<expirationDate><value>2013-10-01</value>
</expirationDate>
<underlyingSecurity><underlyingSecurityTitle><value>Common Stock</value>
</underlyingSecurityTitle>
<underlyingSecurityShares><value>20000</value>
<footnoteId id="F1"></footnoteId>
</underlyingSecurityShares>
</underlyingSecurity>
<postTransactionAmounts><sharesOwnedFollowingTransaction><value>20000</value>
<footnoteId id="F1"></footnoteId>
</sharesOwnedFollowingTransaction>
</postTransactionAmounts>
<ownershipNature><directOrIndirectOwnership><value>D</value>
</directOrIndirectOwnership>
</ownershipNature>
</derivativeTransaction>
</derivativeTable>
<footnotes><footnote id="F1">This amendment is being filed to correct the transaction date and to correct the number of shares subject to the stock option, which was erroneously reported on the reporting person's Form 4 filed October 3, 2003 as 10,000 shares.</footnote>
<footnote id="F2">Option vests as follows: 25% vest on 10/1/04; 1/48th vesting monthly following three years.</footnote>
</footnotes>
<ownerSignature><signatureName>/s/ R. William Bowen, Attorney-in-Fact</signatureName>
<signatureDate>2003-12-03</signatureDate>
</ownerSignature>
</ownershipDocument>

