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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>0001209191-09-058376.txt : 20091222
<SEC-HEADER>0001209191-09-058376.hdr.sgml : 20091222
<ACCEPTANCE-DATETIME>20091222165741
ACCESSION NUMBER:		0001209191-09-058376
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20091218
FILED AS OF DATE:		20091222
DATE AS OF CHANGE:		20091222

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			FISHERMAN JASON S
		CENTRAL INDEX KEY:			0001197540

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-33095
		FILM NUMBER:		091255722

	MAIL ADDRESS:	
		STREET 1:		C/O ADVENT INTERNATIONAL CORP
		STREET 2:		75 STATE ST 29TH FLOOR
		CITY:			BOSTON
		STATE:			MA
		ZIP:			02104

ISSUER:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			ACHILLION PHARMACEUTICALS INC
		CENTRAL INDEX KEY:			0001070336
		STANDARD INDUSTRIAL CLASSIFICATION:	PHARMACEUTICAL PREPARATIONS [2834]
		IRS NUMBER:				000000000

	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
</SEC-HEADER>
<DOCUMENT>
<TYPE>4
<SEQUENCE>1
<FILENAME>doc4.xml
<DESCRIPTION>FORM 4 SUBMISSION
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0303</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2009-12-18</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001197540</rptOwnerCik>
            <rptOwnerName>FISHERMAN JASON S</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O ADVENT INTERNATIONAL CORPORATION</rptOwnerStreet1>
            <rptOwnerStreet2>75 STATE STREET</rptOwnerStreet2>
            <rptOwnerCity>BOSTON</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02109</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Stock Option</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>3.28</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2009-12-18</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>20000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0.00</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <value>2019-12-18</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>20000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>20000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">25% of the shares will vest on the first anniversary of the date of the grant.  6.25% of the shares will vest at the end of each three month period thereafter.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Jason S. Fisherman</signatureName>
        <signatureDate>2009-12-22</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
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