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    <periodOfReport>2020-01-28</periodOfReport>

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    <issuer>
        <issuerCik>0001070336</issuerCik>
        <issuerName>ACHILLION PHARMACEUTICALS INC</issuerName>
        <issuerTradingSymbol>ACHN</issuerTradingSymbol>
    </issuer>

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        <reportingOwnerId>
            <rptOwnerCik>0001452429</rptOwnerCik>
            <rptOwnerName>Truitt Joseph</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O ACHILLION PHARMACEUTICALS, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>1777 SENTRY PARKWAY W, BLDG 14, STE 200</rptOwnerStreet2>
            <rptOwnerCity>BLUE BELL</rptOwnerCity>
            <rptOwnerState>PA</rptOwnerState>
            <rptOwnerZipCode>19422</rptOwnerZipCode>
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            <isOfficer>true</isOfficer>
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            <isOther>false</isOther>
            <officerTitle>Chief Executive Officer</officerTitle>
            <otherText></otherText>
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            <securityTitle>
                <value>Stock Options (Right to buy)</value>
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                <value>2.18</value>
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                <equitySwapInvolved>false</equitySwapInvolved>
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                    <footnoteId id="F2"/>
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                    <value>D</value>
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                <footnoteId id="F2"/>
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            <expirationDate>
                <value>2029-01-23</value>
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                <underlyingSecurityTitle>
                    <value>Common Stock</value>
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    <footnotes>
        <footnote id="F1">Disposed of pursuant to the merger agreement (the &quot;Merger Agreement&quot;) among Achillion Pharmaceuticals, Inc. (&quot;Achillion&quot;), Alexion Pharmaceuticals, Inc. (&quot;Alexion&quot;) and Beagle Merger Sub, Inc. In addition to the cash consideration of $6.30 per share, each shareholder will also receive one contingent value right (&quot;CVR&quot;) per share. Each CVR represents the right to receive contingent cash payments of $1.00 upon the achievement of a certain clinical trial milestone with respect to ACH-5228 and $1.00 upon the achievement of a certain regulatory approval milestone with respect to ACH-4471.</footnote>
        <footnote id="F2">Subject to certain conditions, at the effective time, all unexercised options with an exercise price below $6.30 were cancelled and converted into the right to receive (i) a cash payment of (A) $6.30 less the exercise price, multiplied by (B) the number of shares subject thereto and (ii) one CVR per share subject thereto. Options with an exercise price of $6.30 or greater were cancelled and converted into the right to receive a cash payment with respect to each share subject thereto upon each milestone payment date equal to (i) the amount by which, as of the payment date, the sum of (x) $6.30, (y) the amount per share previously paid in respect of any earlier payment date and (z) the amount in cash to be paid at such payment date exceeds the exercise price payable under such option, less (ii) the amount of all payments previously received with respect to such option. Options with an exercise price of $8.30 or greater were cancelled without any consideration payable therefor.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Keri Lantz, attorney-in-fact</signatureName>
        <signatureDate>2020-01-29</signatureDate>
    </ownerSignature>
</ownershipDocument>
