-----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,
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<SEC-DOCUMENT>0001209191-08-039421.txt : 20080630
<SEC-HEADER>0001209191-08-039421.hdr.sgml : 20080630
<ACCEPTANCE-DATETIME>20080630163221
ACCESSION NUMBER:		0001209191-08-039421
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20080626
FILED AS OF DATE:		20080630
DATE AS OF CHANGE:		20080630

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

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			Park Todd Y.
		CENTRAL INDEX KEY:			0001412136

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-33689
		FILM NUMBER:		08926228

	BUSINESS ADDRESS:	
		BUSINESS PHONE:		617-402-1000

	MAIL ADDRESS:	
		STREET 1:		ATHENAHEALTH, INC.
		STREET 2:		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>2008-06-26</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001412136</rptOwnerCik>
            <rptOwnerName>Park Todd Y.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O ATHENAHEALTH, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>311 ARSENAL STREET</rptOwnerStreet2>
            <rptOwnerCity>WATERTOWN</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02472</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>2008-06-26</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>S</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
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            <transactionTimeliness>
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            <transactionAmounts>
                <transactionShares>
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                    <footnoteId id="F1"/>
                </transactionShares>
                <transactionPricePerShare>
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                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>916000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
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            <transactionDate>
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                <sharesOwnedFollowingTransaction>
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                </sharesOwnedFollowingTransaction>
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            <transactionDate>
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                <sharesOwnedFollowingTransaction>
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            <transactionDate>
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            <transactionCoding>
                <transactionFormType>4</transactionFormType>
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                <transactionPricePerShare>
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                <transactionAcquiredDisposedCode>
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        <nonDerivativeTransaction>
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                <value>Common Stock</value>
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            <transactionDate>
                <value>2008-06-26</value>
            </transactionDate>
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                <transactionCode>S</transactionCode>
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            <transactionTimeliness>
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            </transactionTimeliness>
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                <transactionShares>
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                    <footnoteId id="F1"/>
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                <transactionPricePerShare>
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                <transactionAcquiredDisposedCode>
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                <sharesOwnedFollowingTransaction>
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                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
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            <transactionDate>
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            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
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            <transactionTimeliness>
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                <transactionShares>
                    <value>100</value>
                    <footnoteId id="F1"/>
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                <transactionPricePerShare>
                    <value>30.34</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
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                <sharesOwnedFollowingTransaction>
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                </sharesOwnedFollowingTransaction>
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        <nonDerivativeTransaction>
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            <transactionDate>
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            </transactionDate>
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            <transactionTimeliness>
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                <transactionShares>
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                    <footnoteId id="F1"/>
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                <transactionPricePerShare>
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                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
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                <sharesOwnedFollowingTransaction>
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                </sharesOwnedFollowingTransaction>
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            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
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        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
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            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>S</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
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            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>150</value>
                    <footnoteId id="F1"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>29.94</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>915050</value>
                </sharesOwnedFollowingTransaction>
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            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
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        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
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            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
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                <transactionFormType>4</transactionFormType>
                <transactionCode>S</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
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            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>100</value>
                    <footnoteId id="F1"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>29.80</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
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                <sharesOwnedFollowingTransaction>
                    <value>914950</value>
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                    <value>D</value>
                </directOrIndirectOwnership>
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        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2008-06-26</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>29.51</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>914850</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <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 January 7, 2008 in accordance with SEC Rule 10b5-1.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Carl B. Byers
Attorney-in-Fact</signatureName>
        <signatureDate>2008-06-30</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
-----END PRIVACY-ENHANCED MESSAGE-----