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Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
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 qlBrq2ou6t38l23b/xqw/g==

<SEC-DOCUMENT>0001209191-09-045206.txt : 20090921
<SEC-HEADER>0001209191-09-045206.hdr.sgml : 20090921
<ACCEPTANCE-DATETIME>20090921165415
ACCESSION NUMBER:		0001209191-09-045206
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20090917
FILED AS OF DATE:		20090921
DATE AS OF CHANGE:		20090921

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			Byers Carl B.
		CENTRAL INDEX KEY:			0001412135

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-33689
		FILM NUMBER:		091079252

	MAIL ADDRESS:	
		STREET 1:		ATHENAHEALTH, INC.
		STREET 2:		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>
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    <schemaVersion>X0303</schemaVersion>

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    <periodOfReport>2009-09-17</periodOfReport>

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    <issuer>
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        <issuerName>ATHENAHEALTH INC</issuerName>
        <issuerTradingSymbol>ATHN</issuerTradingSymbol>
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            <rptOwnerName>Byers Carl B.</rptOwnerName>
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            <rptOwnerStreet2>311 ARSENAL STREET</rptOwnerStreet2>
            <rptOwnerCity>WATERTOWN</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02472</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
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            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>SVP and CFO</officerTitle>
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            <transactionDate>
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                    <footnoteId id="F1"/>
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                <transactionPricePerShare>
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                <transactionAcquiredDisposedCode>
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            <securityTitle>
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            <transactionDate>
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                    <footnoteId id="F1"/>
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                <transactionPricePerShare>
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                <transactionShares>
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                    <footnoteId id="F1"/>
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                <transactionAcquiredDisposedCode>
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                    <footnoteId id="F1"/>
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                    <footnoteId id="F1"/>
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            <transactionAmounts>
                <transactionShares>
                    <value>100</value>
                    <footnoteId id="F1"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>39.50</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
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            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>213505</value>
                </sharesOwnedFollowingTransaction>
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                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
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        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2009-09-17</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>S</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>100</value>
                    <footnoteId id="F1"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>39.36</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>213405</value>
                </sharesOwnedFollowingTransaction>
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            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2009-09-17</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>S</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>100</value>
                    <footnoteId id="F1"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>39.14</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>213305</value>
                </sharesOwnedFollowingTransaction>
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            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">The sales reported on this Form 4 were made pursuant to a written trading plan adopted by the Reporting Person on December 16, 2008, in accordance with Rule 10b5-1.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Daniel H. Orenstein
Attorney-in-Fact</signatureName>
        <signatureDate>2009-09-21</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
-----END PRIVACY-ENHANCED MESSAGE-----