<PAGE>

                                                                   EXHIBIT 10.14

                          REGISTRATION RIGHTS AGREEMENT

     THIS REGISTRATION RIGHTS AGREEMENT is entered into as of September 9, 1999,
by and between Silicon Valley Bank ("Purchaser") and Athena Healthcare
Incorporated, a Delaware corporation ("Company").

                                    RECITALS

     A. Concurrently with the execution of this Agreement, the Purchaser is
acquiring from the Company a warrant (the "Warrant") pursuant to which Purchaser
has the right to acquire from the Company the Eligible Shares (as defined in the
Warrant).

     B. By this Agreement, the Purchaser and the Company desire to set forth the
registration rights of the Shares all as provided herein.

          NOW, THEREFORE, in consideration of the mutual promises, covenants and
conditions hereinafter set forth, the parties hereto mutually agree as follows:

     1. Registration Rights. The Company covenants and agrees as follows:

          1.1 Definitions. For purposes of this Section 1:

               (a) The term "register," "registered," and "registration" refer
to a registration effected by preparing and filing a registration statement or
similar document in compliance with the Securities Act of 1933, as amended, and
the rules and regulations thereunder (the "Securities Act"), and the declaration
or ordering of effectiveness of such registration statement or document;

               (b) The term "Registrable Securities" means (i) the Eligible
Shares (as defined in the Warrant) issued or issuable upon exercise of the
Warrant and (ii) any Common Stock of the Company issued as (or issuable upon the
conversion or exercise of any warrant, right or other security which is issued
as) a dividend or other distribution with respect to, or in exchange for or in
replacement of, any stock referred to in (i).

               (c) The terms "Holder" or "Holders" means the Purchaser or
qualifying transferees under subsection 1.8 hereof who hold Registrable
Securities.

               (d) The term "SEC" means the Securities and Exchange Commission.

               (e) The terms "Form S-1," Form S-3" etc. shall mean those forms
with such designations as are required by the SEC and any successor or
replacement forms adopted by the SEC.

          1.2 Company Registration.

               (a) Registration. If at any time or from time to time, the
Company shall determine to register any of its securities, for its own account
or the account of any of its shareholders, other than a registration on Form S-8
relating solely to employee stock option or purchase plans or on Form S-4
relating solely to an SEC Rule 145 transaction, the Company will:

                    (i) promptly give to each Holder written notice thereof
(which shall include a list of the jurisdictions in which the Company intends to
attempt to qualify such securities under the applicable blue sky or other state
securities laws); and

<PAGE>

                    (ii) include in such registration (and qualifications), and
in any underwriting involved therein, all the Registrable Securities specified
in a written request or requests, made within 30 days after receipt of such
written notice from the Company, by any Holder or Holders, except as set forth
in subsection 1.2(b) below.

               (b) Underwriting. If the registration of which the Company gives
notice is for a registered public offering involving an underwriting, the
Company shall so advise the Holders as a part of the written notice given
pursuant to subsection 1.2(a)(i). In such event the right of any Holder to
registration pursuant to this subsection 1.2 shall be conditioned upon such
Holder's participation in such underwriting and the inclusion of such Holder's
Registrable Securities in the underwriting to the extent provided herein. All
Holders proposing to distribute their securities through such underwriting shall
(together with the Company and the other shareholders distributing their
securities through such underwriting) enter into an underwriting agreement in
customary form with the underwriter or underwriters selected for such
underwriting by the Company.

               (c) In the case of any registration of Common Stock by the
Company, if the managing underwriters give written advice to the Company that
marketing factors require a limitation on the number of shares of Common Stock
(or other securities convertible into or exchangeable for Common Stock) to be
offered and sold by stockholders of Company in such offering, there shall be
included in the offering: (i) first, all securities proposed by Company to be
sold for its account; and (ii) second, that number of shares Common Stock, if
any, requested to be included in such registration statement by stockholders
(including Holders) of the Company, on a pro rata basis based upon the number of
shares of Common Stock each such stockholder beneficially owns.

          1.3 Expenses of Registration. All expenses incurred in connection with
any registration, qualification or compliance pursuant to this Section 1
including without limitation, all registration, filing and qualification fees,
printing expenses, underwriting fees, discounts and commissions, fees and
disbursements of counsel for the Company and expenses of any special audits
incidental to or required by such registration, shall be borne by the Company.
All expenses of any registered offering not otherwise borne by the Company will
be borne pro rata among the Holders, any other shareholders of the Company
participating in such offering and the Company.

          1.4 Registration Procedures. In the case of each registration,
qualification or compliance effected by the Company pursuant to this
Registration Rights Agreement, the Company will keep each Holder participating
therein advised in writing as to the initiation of each registration,
qualification and compliance and as to the completion thereof. At its expense
the Company will:

               (a) Prepare and file with the SEC a registration statement with
respect to such Registrable Securities and use its best efforts to cause such
registration statement to become effective, and, upon the request of the Holders
of a majority of the Registrable Securities registered thereunder, keep such
registration statement effective for up to 120 days (the "Effective Period).

               (b) Prepare and file with the SEC such amendments and supplements
to such registration statement and the prospectus used in connection with such
registration statement as may be necessary to comply with the provisions of the
Securities Act with respect to the disposition of all securities covered by such
registration statement.

               (c) Furnish to the Holders such numbers of copies of a
prospectus, including a preliminary prospectus, in conformity with the
requirements of the Securities Act, and such other documents as they may
reasonably request in order to facilitate the disposition of Registrable
Securities owned by them.

<PAGE>

               (d) Use its best efforts to register and qualify the securities
covered by such registration statement under such other securities or Blue Sky
laws of such jurisdictions as shall be reasonably requested by the Holders,
provided that the Company shall not be required in connection therewith or as a
condition thereto to qualify to do business or to file a general consent to
service of process in any such states or jurisdictions.

               (e) In the event of any underwritten public offering, enter into
and perform its obligations under an underwriting agreement, in usual and
customary form, with the managing underwriter of such offering. Each Holder
participating in such underwriting shall also enter into and perform its
obligations under such an agreement provided that all other shareholders of the
Company participating in such offering do the same.

               (f) Notify each Holder of Registrable Securities covered by such
registration statement at any time when a prospectus relating thereto is
required to be delivered under the Securities Act or the happening of any event
as a result of which the prospectus included in such registration statement, as
then in effect, includes an untrue statement of a material fact or omits to
state a material fact required to be stated therein or necessary to make the
statements therein not misleading in the light of the circumstances then
existing.

          1.5 Indemnification.

               (a) The Company will indemnify each Holder of Registrable
Securities and each of its officers, directors and partners, and each person
controlling such Holder, with respect to which such registration, qualification
or compliance has been effected pursuant to this Rights Agreement, and each
underwriter, if any, and each person who controls any underwriter of the
Registrable Securities held by or issuable to such Holder, against all claims,
losses, expenses, damages and liabilities (or actions in respect thereto)
arising out of or based on any untrue statement (or alleged untrue statement) of
a material fact contained in any prospectus, offering circular or other document
(including any related registration statement, notification or the like)
incident to any such registration, qualification or compliance, or based on any
omission (or alleged omission) to state therein a material fact required to be
stated therein or necessary to make the statement therein not misleading, or any
violation or alleged violation by the Company of the Securities Act, the
Securities Exchange Act of 1934, as amended, and the rules and regulations
thereunder ("Exchange Act") or any state securities law applicable to the
Company or any rule or regulation promulgated any such state law and relating to
action or inaction required of the Company in connection with any such
registration, qualification or compliance, and will reimburse each such Holder,
each of its officers, directors and partners, and each person controlling such
Holder, each such underwriter and each person who controls any such underwriter,
within a reasonable amount of time after incurred for any reasonable legal and
any other expenses incurred in connection with investigating, defending or
settling any such claim, loss, damage, liability or action; provided, however,
that the indemnity agreement contained in this subsection 1.5(a) shall not apply
to amounts paid in settlement of any such claim, loss, damage, liability, or
action if such settlement is effected without the consent of the Company (which
consent shall not be unreasonably withheld or delayed); and provided further,
that the Company will not be liable in any such case to the extent that any such
claim, loss, damage or liability arises out of or is based on any untrue
statement or omission based upon written information furnished to the Company by
an instrument duly executed by such Holder or underwriter specifically for use
therein.

               (b) Each Holder will, if Registrable Securities held by or
issuable to such Holder are included in the securities as to which such
registration, qualification or compliance is being effected, indemnify the
Company, each of its directors and officers, each underwriter, if any, of the
Company's securities covered by such a registration statement, each person who
controls the Company within the meaning of the Securities Act, and each other
such Holder, each of its officers, directors and partners and each person
controlling such Holder, against all claims, losses, expenses, damages and
liabilities (or actions

<PAGE>

in respect thereof) arising out of or based on any untrue statement (or alleged
untrue statement) of a material fact contained in any such registration
statement, prospectus, offering circular or other document, or any omission (or
alleged omission) to state therein a material fact required to be stated therein
or necessary to make the statements therein not misleading, and will reimburse
the Company, such Holders, such directors, officers, partners, persons or
underwriters for any reasonable legal or any other expenses incurred in
connection with investigating, defending or settling any such claim, loss,
damage, liability or action, in each case to the extent, but only to the extent,
that such untrue statement (or alleged untrue statement) or omission (or alleged
omission) is made in such registration statement, prospectus, offering circular
or other document in reliance upon and in conformity with written information
furnished to the Company by an instrument duly executed by such Holder
specifically for use therein; provided, however, that the indemnity agreement
contained in this subsection 1.5(b) shall not apply to amounts paid in
settlement of any such claim, loss, damage, liability or action if such
settlement is effected without the consent of the Holder, (which consent shall
not be unreasonably withheld or delayed); and provided further, that the total
amount for which any Holder shall be liable under this subsection 1.5(b) shall
not in any event exceed the aggregate proceeds received by such Holder from the
sale of Registrable Securities held by such Holder in such registration.

               (c) Each party entitled to indemnification under this subsection
1.5 (the "Indemnified Party") shall give notice to the party required to provide
indemnification (the "Indemnifying Party") promptly after such Indemnified Party
has actual knowledge of any claim as to which indemnity may be sought, and shall
permit the Indemnifying Party to assume the defense of any such claim or any
litigation resulting therefrom; provided that counsel for the Indemnifying
Party, who shall conduct the defense of such claim or litigation, shall be
approved by the Indemnified Party (whose approval shall not be unreasonably
withheld), and the Indemnified Party may participate in such defense at such
party's expense; and provided further, that the failure of any Indemnified Party
to give notice as provided herein shall not relieve the Indemnifying Party of
its obligations hereunder, unless such failure resulted in prejudice to the
Indemnifying Party; and provided further, that an Indemnified Party (together
with all other Indemnified Parties which may be represented without conflict by
one counsel) shall have the right to retain one separate counsel, with the fees
and expenses to be paid by the Indemnifying Party, if representation of such
Indemnified Party by the counsel retained by the Indemnifying Party would be
inappropriate due to actual or potential differing interests between such
Indemnified Party and any other party represented by such counsel in such
proceeding. No Indemnifying Party, in the defense of any such claim or
litigation, shall, except with the consent of each Indemnified Party, consent to
entry of any judgment or enter into any settlement which does not include as an
unconditional term thereof the giving by the claimant or plaintiff to such
Indemnified Party of a release from all liability in respect to such claim or
litigation.

          1.6 Information by Holder. Any Holder or Holders of Registrable
Securities included in any registration shall promptly furnish to the Company
such information regarding such Holder or Holders and the distribution proposed
by such Holder or Holders as the Company may request in writing and as shall be
required in connection with any registration, qualification or compliance
referred to herein.

          1.7 Rule 144 Reporting. With a view to making available to Holders the
benefits of certain rules and regulations of the SEC which may permit the sale
of the Registrable Securities to the public without registration, the Company
agrees at all times to:

               (a) make and keep public information available, as those terms
are understood and defined in SEC Rule 144, after 90 days after the effective
date of the first registration filed by the Company for an offering of its
securities to the general public;

               (b) file with the SEC in a timely manner all reports and other
documents required of the Company under the Securities Act and the Exchange Act
(at any time after it has become subject to such reporting requirements); and

<PAGE>

               (c) so long as a Holder owns any Registrable Securities, to
furnish to such Holder forthwith upon request a written statement by the Company
as to its compliance with the reporting requirements of said Rule 144 (at any
time after 90 days after the effective date of the first registration statement
filed by the Company for an offering of its securities to the general public),
and of the Securities Act and the Exchange Act (at any time after it has become
subject to such reporting requirements), a copy of the most recent annual or
quarterly report of the Company, and such other reports and documents so filed
by the Company as the Holder may reasonably request in complying with any rule
or regulation of the SEC allowing the Holder to sell any such securities without
registration.

          1.8 Transfer of Registration Rights. Holders' rights to cause the
Company to register their securities and keep information available, granted to
them by the Company under subsections 1.2 and 1.7 may be assigned to a
transferee or assignee of a Holder's Registrable Securities not sold to the
public, provided, that the Company is given written notice by such Holder at the
time of or within a reasonable time after said transfer, stating the name and
address of said transferee or assignee and identifying the securities with
respect to which such registration rights are being assigned.

     2. General.

          2.1 Waivers and Amendments. With the written consent of the record or
beneficial holders of at least a majority of the Registrable Securities, the
obligations of the Company and the rights of the Holders of the Registrable
Securities under this agreement may be waived (either generally or in a
particular instance, either retroactively or prospectively, and either for a
specified period of time or indefinitely), and with the same consent the
Company, when authorized by resolution of its Board of Directors, may enter into
a supplementary agreement for the purpose of adding any provisions to or
changing in any manner or eliminating any of the provisions of this Agreement;
provided, however, that no such modification, amendment or waiver shall reduce
the aforesaid percentage of Registrable Securities without the consent of all of
the Holders of the Registrable Securities. Upon the effectuation of each such
waiver, consent, agreement of amendment or modification, the Company shall
promptly give written notice thereof to the record holders of the Registrable
Securities who have not previously consented thereto in writing. This Agreement
or any provision hereof may be changed, waived, discharged or terminated only by
a statement in writing signed by the party against which enforcement of the
change, waiver, discharge or termination is sought, except to the extent
provided in this subsection 2.1.

          2.2 Governing Law. This Agreement shall be governed in all respects by
the laws of the Commonwealth of Massachusetts as such laws are applied to
agreements between Massachusetts residents entered into and to be performed
entirely within Massachusetts.

          2.3 Successors and Assigns. Except as otherwise expressly provided
herein, the provisions hereof shall inure to the benefit of, and be binding
upon, the successors, assigns, heirs, executors and administrators of the
parties hereto.

          2.4 Entire Agreement. Except as set forth below, this Agreement and
the other documents delivered pursuant hereto constitute the full and entire
understanding and agreement between the parties with regard to the subjects
hereof and thereof.

          2.5 Notices, etc. All notices and other communications required or
permitted hereunder shall be in writing and shall be mailed by first class mail,
postage prepaid, certified or registered mail, return receipt requested,
addressed (a) if to Holder, at such Holder's address(es) as set forth below, or
at such other address(es) as such Holder shall have furnished to the Company in
writing, or (b) if to the Company, at the Company's address set forth below, or
at such other address as the Company shall have furnished to the Holder in
writing.

<PAGE>

          2.6 Severability. In case any provision of this Agreement shall be
invalid, illegal, or unenforceable, the validity, legality and enforceability of
the remaining provisions of this Agreement or any provision of the other
Agreements shall not in any way be affected or impaired thereby.

          2.7 Titles and Subtitles. The titles of the sections and subsections
of this Agreement are for convenience of reference only and are not to be
considered in construing this Agreement.

          2.8 Counterparts. This Agreement may be executed in any number of
counterparts, each of which shall be an original, but all of which together
shall constitute one instrument.

PURCHASER                               COMPANY

SILICON VALLEY BANK                     ATHENA HEALTHCARE INCORPORATED


By:                                     By:
    ---------------------------------       ------------------------------------
Name:                                   Name:
      -------------------------------         ----------------------------------
      (print)                                 (print)
Title:                                  Title:
       ------------------------------          ---------------------------------
Address:                                Address:
         ----------------------------            -------------------------------

         ----------------------------            -------------------------------

         ----------------------------            -------------------------------

copy to: Silicon Valley Bank
         Treasury Department
         3003 Tasman Drive
         MS NC 821
         Santa Clara, CA 95054

<PAGE>

                AMENDMENT NO. 1 TO REGISTRATION RIGHTS AGREEMENT

     THIS AMENDMENT NO.1 TO REGISTRATION RIGHTS AGREEMENT is made as of
March 31, 2000 by and between Silicon Valley Bank ("Purchaser") and Athena
Healthcare Incorporated, a Delaware corporation (the "Company")

                                    RECITALS

     A. Purchaser and the Company executed a Registration Rights Agreement dated
as of September 9, 1999 (the "Agreement").

     B. Concurrently with the execution and delivery of this Amendment No. 1 to
the Agreement, the Company is issuing to the Purchaser a Warrant to Purchase
Stock (the "Second Warrant").

     C. The parties desire that the shares of Common Stock issuable upon the
conversion of the Shares (as defined in the Second Warrant) and/or the Shares,
if same are shares of Common Stock (the "Second Warrant Conversion Shares"), and
certain other securities relating to the Second Warrant Shares, be included
within the rights granted to Purchaser under the Agreement.

     NOW, THEREFORE, in consideration of the premises and for other good and
valuable consideration, the receipt and sufficiency of which are hereby
acknowledged, the parties agree as follows:

     1. Inclusion of Second Warrant Conversion Shares etc. The definition of
"Registrable Securities" in Section 1.1 (b) of the Agreement is hereby deleted
in its entirety and replaced with the following definition:

          "The term "Registrable Securities" means (i) the shares of Common
          Stock issuable upon (A) conversion of the shares of preferred stock
          issuable under (1) that certain Warrant to Purchase Stock issued by
          the Company to Purchaser on Illegible (the "First Warrant") and (2)
          that certain Warrant to Purchase Stock issued by the Company to
          Purchaser on March 31, 2000 (the "Second Warrant"), and (B) exercise
          of the First Warrant and/or the Second Warrant if at any time the
          Shares (as defined in the First Warrant and Second Warrant,
          respectively) are shares of Common Stock, and (ii) any Common Stock of
          the Company issued as (or issuable upon the conversion or exercise of
          any warrant, right or other security which is issued as) a dividend or
          other distribution with respect to, or in exchange for or in
          replacement of. any stock referred to in (i)."

     2. Company Representations and Warranties. The Company represents and
warrants to Purchaser that the Company's execution, delivery and performance of
this Amendment No. 1 to the Agreement (a) has been duly authorized by all
necessary corporate action of the Company's Board of Directors and shareholders,
(b) will not violate the Company's Restated Certificate of

<PAGE>

Incorporation or By-laws, each as amended, (c) will not violate or cause a
breach or default (or an event which with the passage of time or the giving of
notice or both, would constitute a breach or default) under any agreement,
instrument, mortgage, deed of trust or other arrangement to which the Company is
a party or by which it or any of its assets is subject or bound, and (d) does
not require the approval, consent or waiver of or by any third party which
approval, consent or waiver has not been obtained as of the date hereof.

     3. Except as amended hereby, the Agreement shall remain in full force and
effect as originally written.

     IN WITNESS WHEREOF, the parties have caused this Amendment No. 1 to
Registration Rights Agreement to be executed by their duly authorized
representatives as of the date first above written.

SILICON VALLEY BANK                     ATHENAHEALTHCARE INCORPORATED
                                        Now known athenahealth.com, Inc.


By: /s/ Illegible                       By: /s/ Carl Byers
    ---------------------------------       ------------------------------------
Title: SR VP                            Title: CFO, Treasurer


                                       2

<PAGE>

                AMENDMENT NO. 2 TO REGISTRATION RIGHTS AGREEMENT

     THIS AMENDMENT NO. 2 TO REGISTRATION RIGHTS AGREEMENT is made as of
November 4, 2003 by and between ORIX Venture Partners LLC ("ORIX"), Silicon
Valley Bank ("SVB", and collectively with ORIX, the "Purchasers") and
Athenahealth, Inc. (formerly Athena Healthcare Incorporated), a Delaware
corporation (the "Company").

                                    RECITALS

     A. SVB and the Company executed a Registration Rights Agreement, dated as
of September 9, 1999 (the "Agreement").

     B. Concurrently with the execution of the Agreement, SVB acquired from the
Company a certain Warrant to Purchase Stock, dated as of September 9, 1999 (the
"First Warrant").

     C. SVB and the Company executed an Amendment No. 1 to the Agreement, dated
as of March 31, 2000 ("Amendment No. 1").

     D. Concurrently with the execution of Amendment No. 1, SVB acquired from
the Company a certain Warrant to Purchase Stock, dated as of March 31, 2000 (the
"Second Warrant").

     E. Concurrently with the execution and delivery of this Amendment No. 2 to
the Agreement ("Amendment No. 2"), the Company is issuing to SVB a Warrant to
Purchase Stock (the "Third Warrant") and is issuing to ORIX a Warrant to
Purchase Stock (the "Fourth Warrant", and collectively with the First, Second
and Third Warrants, the "Warrants").

     F. The parties desire that the shares of Common Stock issuable upon the
conversion of the Shares (as defined in the Second, Third and Fourth Warrants)
and/or the Shares, if same are shares of Common Stock (the "Second, Third and
Fourth Warrant Conversion Shares"), and certain other securities relating to the
Shares, be included within the rights granted to the Purchasers under this
Agreement.

     G. The Purchasers and the Company desire that ORIX be made a party to the
Agreement, as amended by Amendment No. 1.

     NOW, THEREFORE, in consideration of the premises and for other good and
valuable consideration, the receipt and sufficiency of which are hereby
acknowledged, the parties agree as follows:

     1. ORIX to Made a Party to the Agreement. As of the date hereof, ORIX shall
be included as a party to this Agreement, in addition to the Purchaser and the
Company.

<PAGE>

     2. Inclusion of Second, Third and Fourth Warrant Conversion Shares etc. The
definition of "Registrable Securities" in Section 1.1(b) of the Agreement is
hereby deleted in its entirety and replaced with the following definition:

          "The term "Registrable Securities" means (i) the shares of Common
          Stock issuable upon (A) conversion of the shares of preferred stock
          issuable under (1) that certain Warrant to Purchase Stock issued by
          the Company to Purchaser on September 9, 1999 (the "First Warrant"),
          (2) that certain Warrant to Purchase Stock issued by the Company to
          Purchaser on March 31, 2000 (the "Second Warrant"), (3) that certain
          Warrant to Purchase Stock issued by the Company to ORIX Venture
          Finance LLC ("Orix") on November 4, 2003 (the "Third Warrant") and (4)
          that certain Warrant to Purchase Stock issued by the Company to
          Purchaser on November 4, 2003 (the "Fourth Warrant") and (B) exercise
          of the First Warrant, the Second Warrant, the Third Warrant and/or the
          Fourth Warrant if at any time the Shares (as defined in the First
          Warrant, the Second Warrant, the Third Warrant and the Fourth Warrant,
          respectively) are shares of Common Stock, and (ii) any Common Stock of
          the Company issued as (or issuable upon the conversion or exercise of
          any warrant, right or other security which is issued as) a dividend or
          other distribution with respect to, or in exchange for or in
          replacement of, any stock referred to in (i)."

     3. Inclusion of ORIX as a Holder. The definition of "Holder" and "Holders"
in Section 1.1(c) of the Agreement is hereby deleted in its entirety and
replaced with the following definition:

          "The terms "Holder" or "Holders" means the Purchaser and ORIX or
          qualifying transferees under subsection 1.8 hereof who hold
          Registrable Securities."

     4. Additional Provision. A new Section 2.9 shall be added to the Agreement
as follows:

          "2.9. "Lock-Up" and Market Standstill. Each holder of Registrable
Securities agrees that in the event the Company proposes to offer for sale to
the public any of its equity securities in any registration statement under the
Securities Act (whether for its own account or the account of others, including
the holders of Registrable Securities), and (1) if requested in writing by the
Company and an underwriter of the proposed offering of Common Stock or other
securities of the Company; and (2) if all other "affiliates" and all 5%
stockholders, directors and officers similarly situated are requested by the
Company and such underwriter to sign, and actually do sign, any "Lock-Up
Agreement" (as described herein), then such holder will agree to a restriction
whereby it will not sell, grant any option or right to buy or sell, or otherwise
transfer or dispose of in any manner or in any hedging or other derivative
security transaction, to the public in open market transactions, any Common
Stock or other securities of the Company held by it during whatever time period
requested by the Company and the underwriter for restrictions on trading or
transfer (the "Lock-Up Period") following the effective date of the registration
statement of the Company filed under the Securities Act. Such agreements shall
be in writing and in form and substance pursuant to customary and prevailing
terms and conditions for such Lock-Up Agreements. The Company may impose
stop-transfer instructions with respect to the

<PAGE>

securities subject to the foregoing restrictions until the end of the Lock-Up
Period. Such Lock-Up Period applicable to the holders of Registrable Securities
shall not exceed 180 days in length."

     5. Counterparts. This Amendment No. 3 may be executed in any number of
counterparts, all of which taken together shall constitute one and the same
instrument, and any of the parties hereto may execute this Agreement by signing
any such counterpart.

     6. All other provisions of the Registration Rights Agreement shall remain
unchanged and in full force and effect.

<PAGE>

     IN WITNESS WHEREOF, the parties have caused this Amendment No. 2 to
Registration Rights Agreement to be executed by their duly authorized
representatives as of the date first above written.

SILICON VALLEY BANK                     ORIX VENTURE FINANCE LLC


By: /s/ Naomi B. Herman                 By: /s/ William Bishop
    ---------------------------------       ------------------------------------
Title: Vice President                   Title: Principal


ATHENAHEALTH, INC.


By: /s/ Jonathan Bush
    ---------------------------------
Title: CEO
<PAGE>

                    AMENDMENT NO. 3 TO REGISTRATION RIGHTS AGREEMENT

     THIS AMENDMENT NO. 3 TO REGISTRATION RIGHTS AGREEMENT is made as of
February 28, 2005 by and between ORIX Venture Partners LLC ("ORIX"), Silicon
Valley Bank ("SVB" or "Purchaser", and collectively with ORIX, the "Holders")
and Athenahealth, Inc. (formerly Athena Healthcare Incorporated), a Delaware
corporation (the "Company").

                                    RECITALS

     A. SVB and the Company executed a Registration Rights Agreement, dated as
of September 9, 1999 (as amended, restated, supplemented, or otherwise modified
from time to time, the "Agreement").

     B. Concurrently with the execution of the Agreement, SVB acquired from the
Company a certain Warrant to Purchase Stock, dated as of September 9, 1999 (the
"First Warrant").

     C. SVB and the Company executed an Amendment No. 1 to the Agreement, dated
as of March 31, 2000 ("Amendment No. 1").

     D. Concurrently with the execution of Amendment No. 1, SVB acquired from
the Company a certain Warrant to Purchase Stock, dated as of March 31, 2000 (the
"Second Warrant").

     E. SVB, ORIX, and the Company executed an Amendment No. 2 to the Agreement,
dated as of November 4, 2003 ("Amendment No. 2"), pursuant to which, among other
things, ORIX became a party to the Agreement as an additional Holder.

     F. Concurrently with the execution of Amendment No. 2, SVB acquired from
the Company a certain Warrant to Purchase Stock, dated as of November 4, 2003
(the "Third Warrant"), and ORIX acquired from the Company a certain Warrant to
Purchase Stock, dated as of November 4, 2003 (the "Fourth Warrant").

     G. Concurrently with the execution and delivery of this Amendment No. 3 to
the Agreement ("Amendment No. 3"), the Company is issuing to SVB a Warrant to
Purchase Stock (the "Fifth Warrant") and is issuing to ORIX a Warrant to
Purchase Stock (the "Sixth Warrant", and collectively with the First, Second,
Third, Fourth, and Fifth Warrants, the "Warrants").

     H. The parties desire that the shares of Common Stock issuable upon the
conversion of the Shares (as defined in the Second, Third, Fourth, Fifth, and
Sixth Warrants) and/or the Shares, if same are shares of Common Stock (the
"Second, Third, Fourth, Fifth, and Sixth Warrant Conversion Shares"), and
certain other securities relating to the Shares, be included within the rights
granted to the Holders under the Agreement.


                                       1

<PAGE>

     NOW, THEREFORE, in consideration of the premises and for other good and
valuable consideration, the receipt and sufficiency of which are hereby
acknowledged, the parties agree as follows:

     1. Inclusion of Second, Third, Fourth, Fifth, and Sixth Warrant Conversion
Shares etc. The definition of "Registrable Securities" in Section 1.1(b) of the
Agreement is hereby deleted in its entirety and replaced with the following
definition:

          "The term "Registrable Securities" means (i) the shares of Common
          Stock issuable upon (A) conversion of the shares of preferred stock
          issuable under (1) that certain Warrant to Purchase Stock issued by
          the Company to Purchaser on September 9, 1999 (the "First Warrant"),
          (2) that certain Warrant to Purchase Stock issued by the Company to
          Purchaser on March 31, 2000 (the "Second Warrant"), (3) that certain
          Warrant to Purchase Stock issued by the Company to ORIX Venture
          Finance LLC ("ORIX") on November 4, 2003 (the "Third Warrant"), (4)
          that certain Warrant to Purchase Stock issued by the Company to
          Purchaser on November 4, 2003 (the "Fourth Warrant"), (5) that certain
          Warrant to Purchase Stock issued by the Company to Purchaser on
          February 28, 2005 (the "Fifth Warrant"), and (6) that certain Warrant
          to Purchase Stock issued by the Company to ORIX on February 28, 2005
          (the "Sixth Warrant"), and (B) exercise of the First Warrant, the
          Second Warrant, the Third Warrant, Fourth Warrant, Fifth Warrant,
          and/or the Sixth Warrant if at any time the Shares (as defined in the
          First Warrant, the Second Warrant, the Third Warrant, the Fourth
          Warrant, the Fifth Warrant, and the Sixth Warrant, respectively) are
          shares of Common Stock, and (ii) any Common Stock of the Company
          issued as (or issuable upon the conversion or exercise of any warrant,
          right or other security which is issued as) a dividend or other
          distribution with respect to, or in exchange for or in replacement of,
          any stock referred to in (i)."

     2. Counterparts. This Amendment No. 3 may be executed in any number of
counterparts, all of which taken together shall constitute one and the same
instrument, and any of the parties hereto may execute this Amendment No. 3 by
signing any such counterpart.

     3. All other provisions of the Agreement shall remain unchanged and in full
force and effect.

[remainder of page intentionally left blank; signature page immediately follows]


                                       2

<PAGE>

     IN WITNESS WHEREOF, the parties have caused this Amendment No. 3 to
Registration Rights Agreement to be executed by their duly authorized
representatives as of the date first above written.

SILICON VALLEY BANK                     ORIX VENTURE FINANCE LLC


By: /s/ Illegible                       By: /s/ Kevin P. Sheehan
    ---------------------------------       ---------------------------------
Title: Vice President                   Title: President & CEO


ATHENAHEALTH, INC.


By: /s/ Carl Byers
    ---------------------------------
Title: CFO


<PAGE>

                AMENDMENT NO. 4 TO REGISTRATION RIGHTS AGREEMENT

     THIS AMENDMENT NO. 4 TO REGISTRATION RIGHTS AGREEMENT is made as of
December 28, 2005 by and between ORIX Venture Finance LLC ("ORIX"), SVB
Financial Group (assignee of Silicon Valley Bank) ("SVB" or "Purchaser", and
collectively with ORIX, the "Holders") and athenahealth, Inc. (formerly Athena
Healthcare Incorporated), a Delaware corporation (the "Company").

                                    RECITALS

     A. SVB and the Company executed a Registration Rights Agreement, dated as
of September 9, 1999 (as amended, restated, supplemented, or otherwise modified
from time to time, the "Agreement").

     B. Concurrently with the execution of the Agreement, SVB acquired from the
Company a certain Warrant to Purchase Stock, dated as of September 9, 1999 (the
"First Warrant").

     C. SVB and the Company executed an Amendment No. 1 to the Agreement, dated
as of March 31, 2000 ("Amendment No. 1").

     D. Concurrently with the execution of Amendment No. 1, SVB acquired from
the Company a certain Warrant to Purchase Stock, dated as of March 31, 2000 (the
"Second Warrant").

     E. SVB, ORIX, and the Company executed an Amendment No. 2 to the Agreement,
dated as of November 4, 2003 ("Amendment No. 2"), pursuant to which, among other
things, ORIX became a party to the Agreement as an additional Holder.

     F. Concurrently with the execution of Amendment No. 2, SVB acquired from
the Company a certain Warrant to Purchase Stock, dated as of November 4, 2003
(the "Third Warrant"), and ORIX acquired from the Company a certain Warrant to
Purchase Stock, dated as of November 4, 2003 (the "Fourth Warrant").

     G. Concurrently with the execution and delivery of Amendment No. 3 to the
Agreement dated February 28, 2005 ("Amendment No. 3"), the Company issued to SVB
a certain Warrant to Purchase Stock dated as of February 28, 2005 (the "Fifth
Warrant") and issued to ORIX a certain Warrant to Purchase Stock dated as of
February 28, 2005 (the "Sixth Warrant").

     H. Concurrently with the execution and delivery of this Amendment No. 4 to
the Agreement ("Amendment No. 4"), the Company is issuing to ORIX a Warrant to
Purchase Stock (the "Seventh Warrant", and collectively with the First Warrant,
the Second Warrant, the Third Warrant, the Fourth Warrant, the Fifth Warrant and
the Sixth Warrant, the "Warrants").


                                        1

<PAGE>

     I. The parties desire that the shares of Common Stock issuable upon the
conversion of the Shares (as defined in the Second Warrant, the Third Warrant,
the Fourth Warrant, the Fifth Warrant, the Sixth Warrant and the Seventh
Warrant) and/or the Shares, if same are shares of Common Stock (the "Second,
Third, Fourth, Fifth, Sixth and Seventh Warrant Conversion Shares"), and certain
other securities relating to the Shares, be included within the rights granted
to the Holders under the Agreement.

     NOW, THEREFORE, in consideration of the premises and for other good and
valuable consideration, the receipt and sufficiency of which are hereby
acknowledged, the parties agree as follows:

     1. Inclusion of Second, Third, Fourth, Fifth, Sixth and Seventh Warrant
Conversion Shares etc. The definition of "Registrable Securities" in Section 1.1
(b) of the Agreement is hereby deleted in its entirety and replaced with the
following definition:

     "The term "Registrable Securities" means (i) the shares of Common Stock
     issuable upon (A) conversion of the shares of preferred stock issuable
     under (1) that certain Warrant to Purchase Stock issued by the Company to
     Purchaser on September 9, 1999 (the "First Warrant"), (2) that certain
     Warrant to Purchase Stock issued by the Company to Purchaser on March 31,
     2000 (the "Second Warrant"), (3) that certain Warrant to Purchase Stock
     issued by the Company to ORIX Venture Finance LLC ("ORIX") on November 4,
     2003 (the "Third Warrant"), (4) that certain Warrant to Purchase Stock
     issued by the Company to Purchaser on November 4, 2003 (the "Fourth
     Warrant"), (5) that certain Warrant to Purchase Stock issued by the Company
     to Purchaser on February 28, 2005 (the "Fifth Warrant"), (6) that certain
     Warrant to Purchase Stock issued by the Company to ORIX on February 28,
     2005 (the "Sixth Warrant") and (7) that certain Warrant to Purchase Stock
     issued by the Company to ORIX on December ____, 2005 (the "Seventh
     Warrant"), and (B) exercise of the First Warrant, the Second Warrant, the
     Third Warrant, Fourth Warrant, Fifth Warrant, the Sixth Warrant and/or the
     Seventh Warrant if at any time the Shares (as defined in the First Warrant,
     the Second Warrant, the Third Warrant, the Fourth Warrant, the Fifth
     Warrant, the Sixth Warrant and the Seventh Warrant, respectively) are
     shares of Common Stock, and (ii) any Common Stock of the Company issued as
     (or issuable upon the conversion or exercise of any warrant, right or other
     security which is issued as) a dividend or other distribution with respect
     to, or in exchange for or in replacement of, any stock referred to in (i)."

     2. Counterparts. This Amendment No. 4 may be executed in any number of
counterparts, all of which taken together shall constitute one and the same
instrument, and any of the parties hereto may execute this Amendment No. 4 by
signing any such counterpart.

     3. All other provisions of the Agreement shall remain unchanged and in full
force and effect.

                  [REMAINDER OF PAGE INTENTIONALLY LEFT BLANK]


                                       2

<PAGE>

     IN WITNESS WHEREOF, the parties have caused this Amendment No. 4 to
Registration Rights Agreement to be executed by their duly authorized
representatives as of the date first above written.

SVB FINANCIAL GROUP                     ORIX VENTURE FINANCE LLC
(ASSIGNEE OF SILICON VALLEY BANK)


By: /s/ Illegible                       By: Kevin P. Sheehan
    ---------------------------------       ------------------------------------
Title: TREASURER                        Title: President & CEO


ATHENAHEALTH, INC.


By: /s/ Carl. Byers
    ---------------------------------
Title: Carl. Byers, CFO


                                       3
<PAGE>

                AMENDMENT NO. 5 TO REGISTRATION RIGHTS AGREEMENT

     THIS AMENDMENT NO. 5 TO REGISTRATION RIGHTS AGREEMENT is made as of
September 21, 2006 by and between ORIX Venture Partners LLC ("ORIX"), SVB
Financial Group (assignee of Silicon Valley Bank) ("SVB" or "Purchaser", and
collectively with ORIX, the "Holders") and athenahealth, Inc. (formerly Athena
Healthcare Incorporated), a Delaware corporation (the "Company").

                                    RECITALS

     A. SVB and the Company executed a Registration Rights Agreement, dated as
of September 9, 1999 (as amended, restated, supplemented, or otherwise modified
from time to time, the "Agreement").

     B. Concurrently with the execution of the Agreement, SVB acquired from the
Company a certain Warrant to Purchase Stock, dated as of September 9, 1999 (the
"First Warrant").

     C. SVB and the Company executed an Amendment No. 1 to the Agreement, dated
as of March 31, 2000 "Amendment No. 1").

     D. Concurrently with the execution of Amendment No. 1, SVB acquired from
the Company a certain Warrant to Purchase Stock, dated as of March 31, 2000 (the
"Second Warrant").

     E. SVB, ORIX, and the Company executed an Amendment No. 2 to the Agreement,
dated as of November 4, 2003 ("Amendment No. 2"), pursuant to which, among other
things, ORIX became a party to the Agreement as an additional Holder.

     F. Concurrently with the execution of Amendment No. 2, SVB acquired from
the Company a certain Warrant to Purchase Stock, dated as of November 4, 2003
(the "Third Warrant"), and ORIX acquired from the Company a certain Warrant to
Purchase Stock, dated as of November 4, 2003 (the "Fourth Warrant").

     G. Concurrently with the execution and delivery of Amendment No. 3 to the
Agreement dated February 28, 2005 ("Amendment No. 3"), the Company issued to SVB
a certain Warrant to Purchase Stock dated as of February 28, 2005 (the "Fifth
Warrant") and issued to ORIX a certain Warrant to Purchase Stock dated as of
February 28, 2005 (the "Sixth Warrant").

     H. Concurrently with the execution and delivery of Amendment No. 4 to the
Agreement dated as of December 28, 2005 ("Amendment No. 4"), the Company issued
to ORIX a certain Warrant to Purchase Stock dated as of December 28, 2005 (the
"Seventh Warrant").


                                       1

<PAGE>

     I. Concurrently with the execution of this Amendment No. 5 to the
Agreement, dated as of the date hereof ("Amendment No. 5"), the Company issued
to ORIX a certain Warrant to Purchase Stock, dated as of the date hereof (the
"Eighth Warrant", and collectively with the First Warrant, the Second Warrant,
the Third Warrant, the Fourth Warrant, the Fifth Warrant, the Sixth Warrant, the
Seventh Warrant and the Eighth Warrant, the "Warrants").

     L. The parties desire that the shares of Common Stock issuable upon the
conversion of the Eligible Shares (as defined in the First Warrant), the Shares
(as defined in the Second Warrant, the Third Warrant, the Fourth Warrant, the
Fifth Warrant, the Sixth Warrant, the Seventh Warrant and the Eighth Warrant)
and/or the Shares, if same are shares of Common Stock (the "First, Second,
Third, Fourth, Fifth, Sixth, Seventh and Eighth Warrant Conversion Shares"), and
certain other securities relating to the Shares, be included within the rights
granted to the Holders under the Agreement.

     NOW, THEREFORE, in consideration of the premises and for other good and
valuable consideration, the receipt and sufficiency of which are hereby
acknowledged, the parties agree as follows:

     1. Inclusion of First, Second, Third, Fourth, Fifth, Sixth, Seventh and
Eighth Warrant Conversion Shares. The definition of "Registrable Securities" in
Section 1.1 (b) of the Agreement is hereby deleted in its entirety and replaced
with the following definition:

     "The term "Registrable Securities" means (i) the shares of Common Stock
     issuable upon (A) conversion of the shares of preferred stock issuable
     under (1) that certain Warrant to Purchase Stock issued by the Company to
     Purchaser on September 9, 1999 (the "First Warrant"), (2) that certain
     Warrant to Purchase Stock issued by the Company to Purchaser on March 31,
     2000 (the "Second Warrant"), (3) that certain Warrant to Purchase Stock
     issued by the Company to ORIX Venture Finance LLC ("ORIX") on November 4,
     2003 (the "Third Warrant"), (4) that certain Warrant to Purchase Stock
     issued by the Company to Purchaser on November 4, 2003 (the "Fourth
     Warrant"), (5) that certain Warrant to Purchase Stock issued by the Company
     to Purchaser on February 28, 2005 (the "Fifth Warrant"), (6) that certain
     Warrant to Purchase Stock issued by the Company to ORIX on February 28,
     2005 (the "Sixth Warrant"), (7) that certain Warrant to Purchase Stock
     issued by the Company to ORIX on December 28, 2005 (the "Seventh Warrant"),
     and (8) that certain Warrant to Purchase Stock issued by the Company to
     ORIX on September 21, 2006 (the "Eighth Warrant") and (B) exercise of the
     First Warrant, the Second Warrant, the Third Warrant, Fourth Warrant, Fifth
     Warrant, the Sixth Warrant, the Seventh Warrant and/or the Eighth Warrant
     if at any time the Shares (as defined in the First Warrant, the Second
     Warrant, the Third Warrant, the Fourth Warrant, the Fifth Warrant, the
     Sixth Warrant, the Seventh Warrant and the Eighth Warrant, respectively)
     are shares of Common Stock, and (ii) any Common Stock of the Company issued
     as (or issuable upon the conversion or exercise of any warrant, right or
     other security which is issued as) a dividend or other distribution with
     respect to, or in exchange for or in replacement of, any stock referred to
     in (i)."


                                       2

<PAGE>

     2. Counterparts. This Amendment No. 5 may be executed in any number of
counterparts, all of which taken together shall constitute one and the same
instrument, and any of the parties hereto may execute this Amendment No. 5 by
signing any such counterpart.

     3. All other provisions of the Agreement shall remain unchanged and in full
force and effect.

                  [REMAINDER OF PAGE INTENTIONALLY LEFT BLANK]


                                       3

<PAGE>

     IN WITNESS WHEREOF, the parties have caused this Amendment No. 5 to
Registration Rights Agreement to be executed by their duly authorized
representatives as of the date first above written.

SVB FINANCIAL GROUP                     ORIX VENTURE FINANCE LLC
(ASSIGNEE OF SILICON VALLEY BANK)


By: /s/ Illegible                       By: Kevin P. Sheehan
    ---------------------------------       ------------------------------------
Title: Relationship Manager             Title: President & CEO


ATHENAHEALTH, INC.


By: /s/ Jonathan Bush
    ---------------------------------
Title: Jonathan Bush, President & CEO


                                       4

<PAGE>
                AMENDMENT NO. 6 TO REGISTRATION RIGHTS AGREEMENT

      THIS AMENDMENT NO. 6 TO REGISTRATION RIGHTS AGREEMENT is made as of May
31, 2007 by and between ORIX Venture Partners LLC ("ORIX"), SVB Financial Group
(assignee of Silicon Valley Bank) ("SVB" or "Purchaser", and collectively with
ORIX, the "Holders") and athenahealth, Inc. (formerly Athena Healthcare
Incorporated), a Delaware corporation (the "Company").

                                    RECITALS

      A. SVB and the Company executed a Registration Rights Agreement, dated as
of September 9, 1999 (as amended, restated, supplemented, or otherwise modified
from time to time, the "Agreement").

      B. Concurrently with the execution of the Agreement, SVB acquired from the
c; Company a certain Warrant to Purchase Stock, dated as of September 9, 1999
(the "First Warrant").

      C. SVB and the Company executed an Amendment No. 1 to the Agreement, dated
as of March 31, 2000 ("Amendment No. 1").

      D. Concurrently with the execution of Amendment No. 1, SVB acquired from
the Company a certain Warrant to Purchase Stock, dated as of March 31, 2000 (the
"Second Warrant").

      E. SVB, ORIX, and the Company executed an Amendment No. 2 to the
Agreement, dated as of November 4, 2003 ("Amendment No. 2"), pursuant to which,
among other things, ORIX became a party to the Agreement as an additional
Holder.

      F. Concurrently with the execution of Amendment No. 2, SVB acquired from
the Company a certain Warrant to Purchase Stock, dated as of November 4, 2003
(the "Third Warrant"), and ORIX acquired from the Company a certain Warrant to
Purchase Stock, dated as of November 4, 2003 (the "Fourth Warrant").

      G. Concurrently with the execution and delivery of Amendment No. 3 to the
Agreement dated February 28, 2005 ("Amendment No. 3"), the Company issued to SVB
a certain Warrant to Purchase Stock dated as of February 28, 2005 (the "Fifth
Warrant") and issued to ORIX a certain Warrant to Purchase Stock dated as of
February 28, 2005 (the "Sixth Warrant").

      H. Concurrently with the execution and delivery of Amendment No. 4 to the
Agreement dated as of December 28, 2005 ("Amendment No. 4"), the Company issued
to ORIX a certain Warrant to Purchase Stock dated as of December 28, 2005 (the
"Seventh Warrant").


                                       1
<PAGE>

      I. Concurrently with the execution of this Amendment No. 5 to the
Agreement, dated as of September 21, 2006 ("Amendment No. 5"), the Company
issued to ORIX a certain Warrant to Purchase Stock, dated as of September 21,
2006 (the "Eighth Warrant").

      J. Concurrently with the execution of this Amendment No. 6 to the
Agreement, dated as of the date hereof ("Amendment No. 6"), the Company issued
to ORIX a certain Warrant to Purchase Stock, dated as of the date hereof (the
"Ninth Warrant", and collectively with the First Warrant, the Second Warrant,
the Third Warrant, the Fourth Warrant, the Fifth Warrant, the Sixth Warrant, the
Seventh Warrant, the Eighth Warrant, and the Ninth Warrant, the "Warrants").

      K. The parties desire that the shares of Common Stock issuable upon the
conversion of the Eligible Shares (as defined in the First Warrant), the Shares
(as defined in the Second Warrant, the Third Warrant, the Fourth Warrant, the
Fifth Warrant, the Sixth Warrant, the Seventh Warrant, the Eighth Warrant, and
the Ninth Warrant) and/or the Shares, if same are shares of Common Stock (the
"First, Second, Third, Fourth, Fifth, Sixth, Seventh, Eighth, and Ninth Warrant
Conversion Shares"), and certain other securities relating to the Shares, be
included within the rights granted to the Holders under the Agreement.

      NOW, THEREFORE, in consideration of the premises and for other good and
valuable consideration, the receipt and sufficiency of which are hereby
acknowledged, the parties agree as follows:

      1. Inclusion of First, Second, Third, Fourth, Fifth, Sixth, Seventh,
Eighth, and Ninth Warrant Conversion Shares. The definition of "Registrable
Securities" in Section 1.1(b) of the Agreement is hereby deleted in its entirety
and replaced with the following definition:

      "The term "Registrable Securities" means (i) the shares of Common Stock
      issuable upon (A) conversion of the shares of preferred stock issuable
      under (1) that certain Warrant to Purchase Stock issued by the Company to
      Purchaser on September 9, 1999 (the "First Warrant"), (2) that certain
      Warrant to Purchase Stock issued by the Company to Purchaser on March 31,
      2000 (the "Second Warrant"), (3) that certain Warrant to Purchase Stock
      issued by the Company to ORIX Venture Finance LLC ("ORIX") on November 4,
      2003 (the "Third Warrant"), (4) that certain Warrant to Purchase Stock
      issued by the Company to Purchaser on November 4, 2003 (the "Fourth
      Warrant"), (5) that certain Warrant to Purchase Stock issued by the
      Company to Purchaser on February 28, 2005 (the "Fifth Warrant"), (6) that
      certain Warrant to Purchase Stock issued by the Company to ORIX on
      February 28, 2005 (the "Sixth Warrant"), (7) that certain Warrant to
      Purchase Stock issued by the Company to ORIX on December 28, 2005 (the
      "Seventh Warrant"), and (8) that certain Warrant to Purchase Stock issued
      by the Company to ORIX on September 21, 2006 (the "Eighth Warrant"), and
      (9) that certain Warrant to Purchase Stock issued by the Company to ORIX
      on May , 2007 (the "Ninth Warrant"), and (B) exercise of the First
      Warrant, the Second Warrant, the Third Warrant, Fourth Warrant, Fifth
      Warrant, the Sixth


                                       2
<PAGE>

      Warrant, the Seventh Warrant, the Eighth Warrant, and/or the Ninth Warrant
      if at any time the Shares (as defined in the First Warrant, the Second
      Warrant, the Third Warrant, the Fourth Warrant, the Fifth Warrant, the
      Sixth Warrant, the Seventh Warrant, the Eighth Warrant, and the Ninth
      Warrant, respectively) are shares of Common Stock, and (ii) any Common
      Stock of the Company issued as (or issuable upon the conversion or
      exercise of any warrant, right or other security which is issued as) a
      dividend or other distribution with respect to, or in exchange for or in
      replacement of, any stock referred to in (i)."

      2. Counterparts. This Amendment No. 6 may be executed in any number of
counterparts, all of which taken together shall constitute one and the same
instrument, and any of the parties hereto may execute this Amendment No. 6 by
signing any such counterpart.

      3. All other provisions of the Agreement shall remain unchanged and in
full force and effect.

                  [REMAINDER OF PAGE INTENTIONALLY LEFT BLANK]


                                       3
<PAGE>

      IN WITNESS WHEREOF, the parties have caused this Amendment No. 6 to
Registration Rights Agreement to be executed by their duly authorized
representatives as of the date first above written.

SVB FINANCIAL GROUP (ASSIGNEE OF        ORIX VENTURE FINANCE LLC
SILICON VALLEY BANK)

By: /s/ Norman Cutler                   By: /s/ Kevin P. Sheeha
    ------------------------------          -----------------------------------
Title: Derivatives Manager              Title: President & CEO
       ---------------------------
       Norman Cutler 408.654.7141.

ATHENAHEALTH, INC.

By: /s/ Carl Buyers
    ------------------------------
Title: Treasurer & CFO