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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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 Q+LukiWQavUiGo/vkALrBg==

<SEC-DOCUMENT>0001209191-06-001830.txt : 20060105
<SEC-HEADER>0001209191-06-001830.hdr.sgml : 20060105
<ACCEPTANCE-DATETIME>20060105130149
ACCESSION NUMBER:		0001209191-06-001830
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20060103
FILED AS OF DATE:		20060105
DATE AS OF CHANGE:		20060105

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			Whitaker Raymond J
		CENTRAL INDEX KEY:			0001292970

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-32629
		FILM NUMBER:		06511573

	BUSINESS ADDRESS:	
		BUSINESS PHONE:		(212) 218-6880

	MAIL ADDRESS:	
		STREET 1:		EUCLIDSR PARTNERS
		STREET 2:		45 ROCKEFELLER PLAZA, SUITE 3240
		CITY:			NEW YORK
		STATE:			NY
		ZIP:			10111

ISSUER:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			AVALON PHARMACEUTICALS INC
		CENTRAL INDEX KEY:			0001162192
		STANDARD INDUSTRIAL CLASSIFICATION:	PHARMACEUTICAL PREPARATIONS [2834]
		IRS NUMBER:				522209310

	BUSINESS ADDRESS:	
		STREET 1:		20358 SENECA MEADOWS PARKWAY
		CITY:			GERMANTOWN
		STATE:			MD
		ZIP:			20876
		BUSINESS PHONE:		3015569900

	MAIL ADDRESS:	
		STREET 1:		20358 SENECA MEADOWS PARKWAY
		CITY:			GERMANTOWN
		STATE:			MD
		ZIP:			20876
</SEC-HEADER>
<DOCUMENT>
<TYPE>4
<SEQUENCE>1
<FILENAME>doc4.xml
<DESCRIPTION>FORM 4 SUBMISSION
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0202</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2006-01-03</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0001162192</issuerCik>
        <issuerName>AVALON PHARMACEUTICALS INC</issuerName>
        <issuerTradingSymbol>AVRX</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001292970</rptOwnerCik>
            <rptOwnerName>Whitaker Raymond J</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>20358 SENECA MEADOWS PARKWAY</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>GERMANTOWN</rptOwnerCity>
            <rptOwnerState>MD</rptOwnerState>
            <rptOwnerZipCode>20876</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2006-01-03</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
                <footnoteId id="F1"/>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>1482</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>4.64</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>1482</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">Issued in lieu of cash payment of director fees pursuant to Avalon Pharmaceuticals, Inc.'s Stock Election Policy for Non-employee Director Fees.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Thomas G. David, Esq., Attorney-in-Fact</signatureName>
        <signatureDate>2006-01-05</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
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