<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0303</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2010-01-06</periodOfReport>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001431443</rptOwnerCik>
            <rptOwnerName>Clarus Lifesciences II, L.P.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O CLARUS VENTURES, LLC</rptOwnerStreet1>
            <rptOwnerStreet2>101 MAIN STREET, SUITE 1210</rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02142</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001431439</rptOwnerCik>
            <rptOwnerName>Clarus Ventures II GP, L.P.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O CLARUS VENTURES, LLC</rptOwnerStreet1>
            <rptOwnerStreet2>101 MAIN STREET, SUITE 1210</rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02142</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001431437</rptOwnerCik>
            <rptOwnerName>Clarus Ventures II, LLC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O CLARUS VENTURES, LLC</rptOwnerStreet1>
            <rptOwnerStreet2>101 MAIN STREET, SUITE 1210</rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02142</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001252523</rptOwnerCik>
            <rptOwnerName>LIPTAK ROBERT</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O CLARUS VENTURES, LLC</rptOwnerStreet1>
            <rptOwnerStreet2>101 MAIN STREET, SUITE 1210</rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02142</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001431403</rptOwnerCik>
            <rptOwnerName>Simon Nicholas</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O CLARUS VENTURES, LLC</rptOwnerStreet1>
            <rptOwnerStreet2>101 MAIN STREET, SUITE 1210</rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02142</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001249153</rptOwnerCik>
            <rptOwnerName>HENNER DENNIS</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O CLARUS VENTURES, LLC</rptOwnerStreet1>
            <rptOwnerStreet2>101 MAIN STREET, SUITE 1210</rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02142</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001252522</rptOwnerCik>
            <rptOwnerName>GALAKATOS NICHOLAS</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O CLARUS VENTURES, LLC</rptOwnerStreet1>
            <rptOwnerStreet2>101 MAIN STREET, SUITE 1210</rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02142</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001431408</rptOwnerCik>
            <rptOwnerName>Leiden Jeffrey</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O CLARUS VENTURES, LLC</rptOwnerStreet1>
            <rptOwnerStreet2>101 MAIN STREET, SUITE 1210</rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02142</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001252525</rptOwnerCik>
            <rptOwnerName>WHEELER KURT</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O CLARUS VENTURES, LLC</rptOwnerStreet1>
            <rptOwnerStreet2>101 MAIN STREET, SUITE 1210</rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02142</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001166285</rptOwnerCik>
            <rptOwnerName>STEINMETZ MICHAEL</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O CLARUS VENTURES, LLC</rptOwnerStreet1>
            <rptOwnerStreet2>101 MAIN STREET, SUITE 1210</rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02142</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2010-01-06</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>S</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
                <footnoteId id="F1"/>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>49400</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>3.5027</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>4624167</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By Fund</value>
                    <footnoteId id="F2"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2010-01-07</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>S</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
                <footnoteId id="F1"/>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>3600</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>3.50</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>4620567</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By Fund</value>
                    <footnoteId id="F2"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">The sales reported on this Form 4 were effected pursuant to Rule 10b5-1 trading plan adpoted by Clarus Lifesciences II, L.P. (the &quot;Fund&quot;) on November 1, 2009.</footnote>
        <footnote id="F2">Securities held of record by the Fund.  Clarus Ventures II GP, L.P. (the &quot;GPLP&quot;), as the sole general partner of the Fund, may be deemed to beneficially own certain of the shares held of record by the Fund.  The GPLP disclaims beneficial ownership of all shares held of record by the Fund in which the GPLP does not have an actual pecuniary interest.  Clarus Ventures II, LLC (the &quot;GPLLC&quot;), as the sole general partner of the GPLP, may be deemed to beneficially own certain of the shares held of record by the Fund. Each of Messrs. Galakatos, Henner, Leiden, Liptak, Simon, Steinmetz and Wheeler, as individual Managing Directors of the GPLLC, may be deemed to beneficially own certain of the shares held of record by the Fund.  Each of Messrs. Galakatos, Henner, Leiden, Liptak, Simon, Steinmetz and Wheeler disclaims beneficial ownership of all shares held of record by the Fund in which he does not have an actual pecuniary interest.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>___________________________________ Robert Liptak, Manager of Clarus Ventures II, LLC, general partner of Clarus Ventures II GP, L.P., general partner of Clarus Lifesciences II, L.P.</signatureName>
        <signatureDate>2010-01-08</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>___________________________________ Robert Liptak, Maganer of Clarus Ventures II, LLC, general partner of Clarus Ventures II GP, L.P.</signatureName>
        <signatureDate>2010-01-08</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>___________________________________ Robert Liptak, Manager of Clarus Ventures II, LLC</signatureName>
        <signatureDate>2010-01-08</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>___________________________________ Robert Liptak, as attorney-in-fact for Nicholas Simon</signatureName>
        <signatureDate>2010-01-08</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>___________________________________ Robert Liptak</signatureName>
        <signatureDate>2010-01-08</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>___________________________________ Robert Liptak, as attorney-in-fact for Dennis Henner</signatureName>
        <signatureDate>2010-01-08</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>___________________________________ Robert Liptak, as attorney-in-fact for Nicholas Galakatos</signatureName>
        <signatureDate>2010-01-08</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>___________________________________ Robert Liptak, as attorney-in-fact for Jeffrey Leiden</signatureName>
        <signatureDate>2010-01-08</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>___________________________________ Robert Liptak, as attorney-in-fact for Kurt Wheeler</signatureName>
        <signatureDate>2010-01-08</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>___________________________________ Robert Liptak, as attorney-in-fact for Michael Steinmetz</signatureName>
        <signatureDate>2010-01-08</signatureDate>
    </ownerSignature>
</ownershipDocument>
