-----BEGIN PRIVACY-ENHANCED MESSAGE-----
Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
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 TWSM7vrzLADbmYQaionwg5sDW3P6oaM5D3tdezXMm7z1T+B+twIDAQAB
MIC-Info: RSA-MD5,RSA,
 R7xAHR04/AtUrYV45SD2cYML2NpoBgpOhzdYVY5BvZVqL78Idcc2qT6cEfM0Qlke
 FWUnSGT28WrfpaW68dX3lQ==

<SEC-DOCUMENT>0001209191-05-054200.txt : 20051028
<SEC-HEADER>0001209191-05-054200.hdr.sgml : 20051028
<ACCEPTANCE-DATETIME>20051028114848
ACCESSION NUMBER:		0001209191-05-054200
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20051026
FILED AS OF DATE:		20051028
DATE AS OF CHANGE:		20051028

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			Farmer Glen A
		CENTRAL INDEX KEY:			0001342640

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-32629
		FILM NUMBER:		051162019

	BUSINESS ADDRESS:	
		BUSINESS PHONE:		(301) 556-1099

	MAIL ADDRESS:	
		STREET 1:		20358 SENECA MEADOWS PARKWAY
		CITY:			GERMANTOWN
		STATE:			MD
		ZIP:			20876

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>2005-10-26</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001342640</rptOwnerCik>
            <rptOwnerName>Farmer Glen A</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>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>Controller</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Option</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>6.00</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2005-10-26</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>1375</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0.00</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2006-04-26</value>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F1"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>1375</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>1375</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">The option will expire at the close of business at the Issuer's headquarters on the day before the 10th anniversary of the grant of the option.  The option will expire earlier if the reporting person's service to the Issuer terminates.  If the reporting person's service to the Issuer terminates for any reason, other than death, disability or cause, then the option will expire at the close of business at the Issuer's headquarters on the 90th day after the reporting person's termination date.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Thomas G. David, Esq. (Attorney-in-Fact)</signatureName>
        <signatureDate>2005-10-28</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
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