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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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 +2YJkvYqHBaBnc3m5UpURw==

<SEC-DOCUMENT>0001209191-10-020117.txt : 20100402
<SEC-HEADER>0001209191-10-020117.hdr.sgml : 20100402
<ACCEPTANCE-DATETIME>20100402135732
ACCESSION NUMBER:		0001209191-10-020117
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20100401
FILED AS OF DATE:		20100402
DATE AS OF CHANGE:		20100402

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			Brown Nancy G.
		CENTRAL INDEX KEY:			0001422569

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-33689
		FILM NUMBER:		10727662

	MAIL ADDRESS:	
		STREET 1:		311 ARSENAL STREET
		CITY:			WATERTOWN
		STATE:			MA
		ZIP:			02472

ISSUER:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			ATHENAHEALTH INC
		CENTRAL INDEX KEY:			0001131096
		STANDARD INDUSTRIAL CLASSIFICATION:	SERVICES-BUSINESS SERVICES, NEC [7389]
		IRS NUMBER:				043387530
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			1231

	BUSINESS ADDRESS:	
		STREET 1:		311 ARSENAL STREET
		CITY:			WATERTOWN
		STATE:			MA
		ZIP:			02472
		BUSINESS PHONE:		617-402-1000

	MAIL ADDRESS:	
		STREET 1:		311 ARSENAL STREET
		CITY:			WATERTOWN
		STATE:			MA
		ZIP:			02472
</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>2010-04-01</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0001131096</issuerCik>
        <issuerName>ATHENAHEALTH INC</issuerName>
        <issuerTradingSymbol>ATHN</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001422569</rptOwnerCik>
            <rptOwnerName>Brown Nancy G.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>311 ARSENAL STREET</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>WATERTOWN, MA</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02472</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>SVP, Corporate Development</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2010-04-01</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>10000</value>
                    <footnoteId id="F1"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0.00</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>10000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">These shares represent restricted stock units issued pursuant to the Issuer's 2007 Stock Option and Incentive Plan. Subject to Reporting Person's continued employment with Issuer, the restricted stock units vest in four equal annual installments beginning on February 15, 2011, until fully vested on February 15, 2014.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Daniel H. Orenstein
Attorney-in-Fact</signatureName>
        <signatureDate>2010-04-02</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
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