<ownershipDocument>
    <schemaVersion>X0201</schemaVersion>

    <documentType>3</documentType>
<periodOfReport>2003-12-17</periodOfReport>
    <noSecuritiesOwned>1</noSecuritiesOwned>

    <issuer>
        <issuerCik>0000820237</issuerCik>
        <issuerName>GEN PROBE INC</issuerName>
        <issuerTradingSymbol>GPRO</issuerTradingSymbol>
</issuer>
<reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001273458</rptOwnerCik>
            <rptOwnerName>POWELSON MARK A</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, Worldwide Sales</officerTitle>
<otherText></otherText>
</reportingOwnerRelationship>
</reportingOwner>
<nonDerivativeTable></nonDerivativeTable>
<derivativeTable></derivativeTable>
<footnotes></footnotes>
<ownerSignature><signatureName>/s/ R. William Bowen, Attorney-in-Fact</signatureName>
<signatureDate>2003-12-17</signatureDate>
</ownerSignature>
</ownershipDocument>

