<ownershipDocument>
    <schemaVersion>X0101</schemaVersion>

    <documentType>3</documentType>
<periodOfReport>2003-07-07</periodOfReport>
    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001110009</issuerCik>
        <issuerName>GENAISSANCE PHARMACEUTICALS INC</issuerName>
        <issuerTradingSymbol>GNSC</issuerTradingSymbol>
</issuer>
<reportingOwner><reportingOwnerId>
            <rptOwnerCik>0001206369</rptOwnerCik>
            <rptOwnerName>KLEIN JOSEPH III</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>
<officerTitle></officerTitle>
<otherText></otherText>
</reportingOwnerRelationship>
</reportingOwner>
<derivativeSecurity><securityTitle><value>Common Stock Warrant (Right to Buy)</value>
</securityTitle>
<conversionOrExercisePrice><value>2.0</value>
</conversionOrExercisePrice>
<exerciseDate><value>2003-05-15</value>
</exerciseDate>
<expirationDate><value>2008-05-15</value>
</expirationDate>
<underlyingSecurity><underlyingSecurityTitle><value>Common Stock</value>
</underlyingSecurityTitle>
<underlyingSecurityShares><value>10000</value>
</underlyingSecurityShares>
</underlyingSecurity>
<ownershipNature><directOrIndirectOwnership><value>D</value>
</directOrIndirectOwnership>
</ownershipNature>
</derivativeSecurity>
<footnotes></footnotes>
<ownerSignature><signatureName>/s/ Ben Kaplan with Power of Attorney for Joseph Klein III</signatureName>
<signatureDate>2003-07-09</signatureDate>
</ownerSignature>
</ownershipDocument>

