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Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
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MIC-Info: RSA-MD5,RSA,
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<SEC-DOCUMENT>0001209191-10-044431.txt : 20100830
<SEC-HEADER>0001209191-10-044431.hdr.sgml : 20100830
<ACCEPTANCE-DATETIME>20100830164245
ACCESSION NUMBER:		0001209191-10-044431
CONFORMED SUBMISSION TYPE:	3
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20100820
FILED AS OF DATE:		20100830
DATE AS OF CHANGE:		20100830

ISSUER:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			ACHILLION PHARMACEUTICALS INC
		CENTRAL INDEX KEY:			0001070336
		STANDARD INDUSTRIAL CLASSIFICATION:	PHARMACEUTICAL PREPARATIONS [2834]
		IRS NUMBER:				000000000
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			1231

	BUSINESS ADDRESS:	
		STREET 1:		300 GEORGE STREET
		CITY:			NEW HAVEN
		STATE:			CT
		ZIP:			06511
		BUSINESS PHONE:		203-624-7000

	MAIL ADDRESS:	
		STREET 1:		300 GEORGE STREET
		CITY:			NEW HAVEN
		STATE:			CT
		ZIP:			06511

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			Quaker BioVentures II LP
		CENTRAL INDEX KEY:			0001497725
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			1231

	FILING VALUES:
		FORM TYPE:		3
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-33095
		FILM NUMBER:		101047204

	BUSINESS ADDRESS:	
		STREET 1:		QUAKER BIOVENTURES
		STREET 2:		2929 ARCH STREET
		CITY:			PHILADELPHIA
		STATE:			PA
		ZIP:			19104
		BUSINESS PHONE:		(215) 988-6800

	MAIL ADDRESS:	
		STREET 1:		QUAKER BIOVENTURES
		STREET 2:		2929 ARCH STREET
		CITY:			PHILADELPHIA
		STATE:			PA
		ZIP:			19104
</SEC-HEADER>
<DOCUMENT>
<TYPE>3
<SEQUENCE>1
<FILENAME>c05448_3x0.xml
<DESCRIPTION>MAIN DOCUMENT DESCRIPTION
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0203</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2010-08-20</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001497725</rptOwnerCik>
            <rptOwnerName>Quaker BioVentures II LP</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O QUAKER BIOVENTURES II, L.P.</rptOwnerStreet1>
            <rptOwnerStreet2>2929 ARCH STREET</rptOwnerStreet2>
            <rptOwnerCity>PHILADELPHIA</rptOwnerCity>
            <rptOwnerState>PA</rptOwnerState>
            <rptOwnerZipCode>19104</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>4859438</value>
                    <footnoteId id="F1"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Warrants to Purchase Common Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>3.1125</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2010-08-20</value>
            </exerciseDate>
            <expirationDate>
                <value>2017-08-20</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>1700803</value>
                    <footnoteId id="F1"/>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">The securities are deemed to be beneficially owned by Quaker BioVentures II, L.P.  Quaker BioVentures Capital II, L.P. is the general partner of Quaker BioVentures II, L.P.  Quaker BioVentures Capital II, LLC is the general partner of Quaker BioVentures Capital II, L.P.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>Quaker BioVentures II, L.P., By: Quaker BioVentures Capital II, L.P., its general partner, By: Quaker BioVentures Capital II, LLC, its general partner, By: /s/ Richard S. Kollender, Vice President</signatureName>
        <signatureDate>2010-08-30</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
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