Document:

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                                                                    EXHIBIT 10.3

                              SECOND AMENDMENT TO
                         REGISTRATION RIGHTS AGREEMENT

          As of this 9th day of October, 1998, that certain Registration Rights
Agreement (the "Agreement") dated December 18, 1997, as amended August 20,1998,
by and among IntraLinks, Inc. (the "Company") and the shareholder signatories
thereto (the "Investors") is hereby amended (the "Amendment") as follows and all
other provisions of the Agreement remain in full force and effect.  All
capitalized terms used herein shall have the meanings assigned to such terms in
the Agreement unless otherwise defined herein.

          "Restricted Stock" shall mean the shares of Common Stock, Series A
Preferred Stock, Series B Preferred Stock, options and warrants listed on
Exhibit A to the Agreement.
---------

          Section 2 shall be deleted in its entirety and replaced with the
following:

          2.  Required Registration.
              ---------------------

          (a) At any time on or after the Earliest Demand Date (as defined
below), Investors holding in the aggregate at least 30% of the Restricted Stock
(as adjusted for stock splits, stock dividends, recapitalizations and the like)
may request, in writing, that the Company effect the registration of Restricted
Stock having an anticipated aggregate offering price of at least $2.0 million
(based on the then current market price or fair value and including any shares
to be registered pursuant to any incidental registration rights described in
paragraph 2(b) hereof) in accordance with the intended methods of distribution
as specified by the Investors in such notice; provided, however, that the only
                                              --------  -------
securities which the Company shall be required to register pursuant hereto shall
be shares of Common Stock. A "Qualified IPO" shall mean the completion of a firm
commitment initial public offering of the Company's Common Stock. "Earliest
Demand Date" shall mean the later of (i) the date eighteen (18) months after a
Qualified IPO (as defined herein) of the Company or (ii) the date six months
after the effectiveness of the first registration statement pursuant to Section
2 of the Series C Registration Rights Agreement (as defined below), so long as
such first registration statement is filed within such 18-month period.

          (b) Promptly following receipt of any notice under Section 2(a), the
Company shall immediately notify (the "Company Notice") all holders of
Restricted Stock and other securityholders who have incidental registration
rights pursuant hereto or to the Registration Rights Agreement (the "Series C
Registration Rights Agreement") dated October 9, 1998 (the shares requested to
be registered pursuant to the Registration Rights Agreement dated October 9,
1998 are referred to herein as the "Additional Shares") and shall use its best
efforts to register under the Securities Act, for public sale in accordance with
the method of disposition specified in the notice from the Investors, the number
of shares of Restricted Stock specified in such notice (and in any notices
received from other holders of Restricted Stock within 20 days after their
receipt of such notice from the Company) and any Additional Shares which the
Company
<PAGE>

is notified of within 20 days of the Company Notice. The Company shall be
entitled to include in any registration statement referred to in this Section 2
shares of Common Stock to be sold by the Company for its own account.
Notwithstanding the foregoing, if the proposed method of disposition specified
by the Investors shall be an underwritten public offering, the number of shares
of Restricted Stock and Additional Shares to be included in such an offering
will be reduced, first by the Company with respect to shares it wishes to
register in such registration (if such registration is the first demand
registration requested by the holders of the Restricted Stock or Additional
Shares) and then pro rata among the requesting holders of Restricted Stock and
                 --------
Additional Shares, based on the total number of shares of Restricted Stock and
Additional Shares so requested to be registered, if and to the extent that the
managing underwriter shall be of the opinion that such inclusion would adversely
affect the marketing of the Restricted Stock and Additional Shares to be sold.
If such method of disposition shall be an underwritten public offering, a
majority of the holders of the Restricted Shares may designate the managing
underwriter of such offering. Notwithstanding the foregoing, the Company shall
be cut back pro rata with the holders of the Restricted Stock and Additional
Shares where the registration is not the first demand registration requested by
either the holders of the Restricted Stock or the holders of the Additional
Shares.

          (c) The Company shall not be required to effect more than one
registration pursuant to Section 2(a) above. In addition, the Company shall not
be obligated to effect any such registration, qualification or compliance
pursuant to this Agreement and the Series C Registration Rights Agreement more
than once in any six (6) month period. Subject to the foregoing, the Company
shall file a registration statement covering the Restricted Stock so requested
to be registered as soon as practicable after receipt of the request or requests
of the holders of the Restricted Stock. Anything to the contrary in this Section
2 notwithstanding, a registration shall not be effected pursuant to this Section
2 with respect to any Restricted Stock once such Restricted Stock otherwise may
be sold to the public without restriction.

          (d) Notwithstanding anything to the contrary contained in this Section
2, in the event that there is a firm commitment underwritten public offering of
securities of the Company pursuant to a registration statement covering
Restricted Stock and a holder of Restricted Stock does not elect to sell his
Restricted Stock to the underwriters of the Company's securities in connection
with such offering, such holder shall agree to refrain from selling or otherwise
transferring its Restricted Stock for a period, to be determined by the managing
underwriter of the offering, of up to 180 days provided that the Company's
shares and any cut-back shares are subject to the same lock-up period.

          Section 4 shall be deleted in its entirety and replaced with the
following:

          4.  Incidental Registration.  If the Company at any time (other than
              -----------------------
pursuant to Section 2 hereof) proposes to register any of its Common Stock under
the Securities Act for sale to the public, whether for its own account or for
the account of other securityholders or both (except with respect to (i)
registration statements on Form S-4 or S-8 or another form not available for
registering the Restricted Stock for sale to the public and (ii) the
registration

                                      -2-
<PAGE>

statement filed pursuant to the first demand exercised pursuant to the Series C
Registration Rights Agreement), it will give written notice at such time to all
holders of outstanding Restricted Stock of its intention to do so. Upon the
written request of any such holder, given within 30 days after receipt of any
such notice by the Company, to register any of its Restricted Stock (which
request shall state the intended method of disposition thereof), the Company
will use its best efforts to cause the Restricted Stock as to which registration
shall have been so requested to be included in the securities to be covered by
the registration statement proposed to be filed by the Company, all to the
extent requisite to permit the sale or other disposition by the holder (in
accordance with its written request) of such Restricted Stock so registered;
provided that nothing herein shall prevent the Company from abandoning or
--------
delaying such registration at any time.  In the event that any registration
pursuant to this Section 4 shall be, in whole or in part, an underwritten public
offering of Common Stock, any request by a holder pursuant to this Section 4 to
register Restricted Stock shall specify that either (i) such Restricted Stock is
to be included in the underwriting on the same terms and conditions as the
shares of Common Stock otherwise being sold through underwriters under such
registration or (ii) such Restricted Stock is to be sold in the open market
without any underwriting, on terms and conditions comparable to those normally
applicable to offerings of common stock in reasonably similar circumstances.
The number of shares of Restricted Stock to be included in such an underwriting
may be reduced (pro rata among the requesting holders of Restricted Stock and
                --- ----
other requesting securityholders who request pursuant to their demand or
incidental registration rights or other similar rights, based upon the total
number of shares so requested to be registered) if and to the extent that the
managing underwriter shall be of the opinion that such inclusion would adversely
affect the marketing of the securities to be sold by the Company therein.

          Notwithstanding anything to the contrary contained in this Section 4,
in the event that there is a firm commitment underwritten public offering of
securities of the Company pursuant to a registration covering Restricted Stock
and a holder of Restricted Stock does not elect to sell his Restricted Stock to
the underwriters of the Company's securities in connection with such offering,
such holder shall agree to refrain from selling or otherwise transferring its
Restricted Stock for a period, to be determined by the managing underwriter, of
up to 180 days.

          This Amendment may be executed in one or more counterparts, each of
which shall be deemed an original, but all of which together shall constitute
one and the same instrument.

                                      -3-
<PAGE>

          Please indicate your acceptance of the foregoing by signing and
returning the enclosed counterpart of this Amendment, whereupon this Amendment
shall be a binding agreement between the Company and you.

                              Very truly yours,

                              INTRALINKS, INC.

                              By: /s/
                                 -------------------------------
                                Name:
                                Title:

AGREED TO AND ACCEPTED as of
the date first above written:

                                                /s/ Sarah Brown-Adams
                                                ----------------------------
EUCLID PARTNERS IV, L.P.                        Sarah Brown-Adams
By: Euclid Associates IV, L.P.

By: /s/                                         WALKER BROWN-ADAMS TRUST
   ----------------------------
Its: General Partner
Name:
Title:                                          By: /s/ Barnett Brown
                                                   --------------------------
                                                   Name:  Barnett Brown
                                                   Title: Trustee
PERSEUS CAPITAL, LLC

                                                /s/ D. W. Brown
                                                ----------------------------
By: /s/ William B. Ford                         Duncan W. Brown
   ----------------------------
Name:  William B. Ford
Title: Senior Vice President

                                                /s/ John M. Muldoon
                                                ----------------------------
CATALYST INVESTMENTS (BELGIUM) N.V.             John M. Muldoon

By:  /s/                                        KELLY JEAN MULDOON TRUST
    -----------------------------
Name:  Mees Pierson Trust (Belgie) N.V.
Title: Managing Director
       J. Hereijgers B.V.B.A                    By: /s/ David T. Muldoon
       De heer J. Hereijgers                       ----------------------------
                                                Name:  David T. Muldoon
                                                Title: Trustee

                                      -4-
<PAGE>

RYAN JOHN MULDOON TRUST                       SCULLEY FAMILY TRUST

By: /s/ David T. Muldoon                     By:  _____________________________
    -----------------------------
    Name:  David T. Muldoon                       Name:
    Title: Trustee                                Title:

ERIC JAMES MULDOON TRUST                      SCULLEY BROTHERS LLC

By: /s/ David T. Muldoon                     By:  /s/ Arthur B. Sculley
    -----------------------------                 -----------------------------
    Name:  David T. Muldoon                       Name:  Arthur B. Sculley
    Title: Trustee                                Title: President

                                              /s/ Patrick J. Wack Jr.
__________________________________            ----------------------------------
Frederick Benjamin                            Patrick J. Wack, Jr.

                                              PATRICK J. WACK, JR. FAMILY TRUST

__________________________________
Ruth Benjamin

                                              By: /s/ Lynda Mulligan
__________________________________                ------------------------------
Eugene A. Tomei                                   Name:  Lynda Mulligan, Pres.
                                                  Title: Rhodes & O'Neill, LLC,
                                                         Trustee

/s/ Arthur B. Sculley                         /s/ Cheryl Snyder
----------------------------------            ----------------------------------
Arthur B. Sculley                             Cheryl Snyder

                                              /s/ Robert L. Lerner
__________________________________            ----------------------------------
David W. Sculley                              Robert Lerner

                                              INCLUSIVE VENTURES LLC

/s/ John Sculley
----------------------------------
John Sculley

                                              By: /s/
                                                  ------------------------------
                                                  Name:
                                                  Title:
<PAGE>

GREENWICH VENTURES LP                           SCULLEY INVESTMENT LTD.
                                                PARTNERSHIP

By: /s/ Jon Victor                              By: /s/ John Sculley
    -------------------------------                 ----------------------------
   Name: Jon Victor                                 Name:
   Title: Manager, Greenwich Ventures, LLC          Title:
          General Partner
          Greenwich Ventures, LP

VANTAGE VENTURES CV

By: /s/ Jon Victor
    -------------------------------
    Name: Jon Victor
    Title: Manager, Greenwich Ventures, LLC
           Investment Partner
           Vantage Ventures CV

LANDWELL FINANCIAL SERVICES, INC.

By: _______________________________
    Name:
    Title:

/s/ Isabel M. Espina
-----------------------------------
Isabel M. Espina

JOHN SCULLEY IRREVOCABLE TRUST
FOR THE BENEFIT OF MADELINE ALLNATT

By: /s/ John Sculley
    -------------------------------
    Name:
    Title:

JOHN SCULLEY IRREVOCABLE TRUST
FOR THE BENEFIT OF OLIVER ALLNATT

By: /s/ John Sculley
    -------------------------------
    Name:
    Title:<PAGE>

                                                                    EXHIBIT 10.4

            THIRD AMENDED AND RESTATED REGISTRATION RIGHTS AGREEMENT
                                INTRALINKS, INC.

          This Third Amended and Restated Registration Rights Agreement (the
"Agreement") is made and entered into as of January 24, 2000 by and among
IntraLinks, Inc., a Delaware corporation (the "Company"), the persons named at
the foot hereof under the caption "Series F Investors" (collectively, the
"Series F Investors"), the persons named at the foot hereof under the caption
"Series E Investors" (collectively, the "Series E Investors"), Ernst & Young
U.S. LLP (the "Series D Investor") and the persons named at the foot hereof
under the caption "Series C Investors" (collectively, the "Series C Investors"
and, together with the Series F Investors, Series E Investors and the Series D
Investor, the "Investors").  This Agreement provides for the registration rights
of the investors in the Company's Series C Convertible Preferred Stock, par
value $.01 (the "Series C Preferred Stock"), Series D Convertible Preferred
Stock, par value $.01 (the "Series D Preferred Stock"), Series E Convertible
Preferred Stock, par value $.01 (the "Series E Preferred Stock") and Series F
Convertible Preferred Stock, par value $.01 (the "Series F Preferred Stock"),
who are signatories hereto.

          In connection with the Investors executing an agreement dated as of
the date hereof with the Company with respect to the acquisition concurrently
herewith of Series F Preferred Stock and the amendment and restatement of that
certain Second Amended and Restated Registration Rights Agreement dated as of
June 30, 1999 by and among the Company, the Series C Investors, the Series D
Investor and the Series E Investors, the Company hereby covenants and agrees
with the Investors and with each subsequent holder of Restricted Stock (as such
term is defined herein) as follows:

          1.   Certain Definitions.  As used herein, the following terms shall
               -------------------
have the following respective meanings:

          "Commission" shall mean the Securities and Exchange Commission, or any
           ----------
     other federal agency at the time administering the Securities Act.

          "Common Stock" shall mean the Common Stock of the Company, $.01 par
           ------------
     value, as constituted as of the date of this Agreement, subject to
     adjustment pursuant to the provisions of Section 8 hereof.

          "Exchange Act" shall mean the Securities Exchange Act of 1934 or any
           ------------
     similar federal statute, and the rules and regulations of the Commission
     thereunder, all as the same shall be in effect at the time.

          "Registration Expenses" shall mean the expenses so described in
           ---------------------
     Section 6 hereof.

          "Restricted Stock" shall mean any shares of Series C Preferred Stock,
           ----------------
     Series D Preferred Stock, Series E Preferred Stock or Series F Preferred
     Stock or any shares of Common Stock issued upon conversion of such shares,
     in each case which are not freely tradable under the Securities Act.
<PAGE>

          "Securities Act" shall mean the Securities Act of 1933 or any similar
           --------------
     federal statute, and the rules and regulations of the Commission
     thereunder, all as the same shall be in effect at the time.

          "Selling Expenses" shall mean the expenses so described in Section 6
           ----------------
hereof.

          2.  Required Registration.
              ---------------------

          (a) At any time on or after the first anniversary of a Qualified IPO
(as defined herein) of the Company, Investors holding in the aggregate at least
30% of the Restricted Stock (as adjusted for stock splits, stock dividends,
recapitalizations and the like) may request, in writing, that the Company effect
the registration of Restricted Stock having an anticipated aggregate offering
price of at least $2.0 million (based on the then current market price or fair
value and including any shares to be registered pursuant to any incidental
registration rights described in paragraph 2(b) hereof) in accordance with the
intended methods of distribution as specified by the Investors in such notice;
provided, however, that the only securities which the Company shall be required
--------  -------
to register pursuant hereto shall be shares of Common Stock.  A "Qualified IPO"
shall mean the completion of a firm commitment initial public offering of the
Company's Common Stock.

          (b) Promptly following receipt of any notice under Section 2(a), the
Company shall immediately notify (the "Company Notice") all holders of
Restricted Stock and all other securityholders that pursuant to the Registration
Rights Agreement (the "1997 Registration Rights Agreement") dated December 18,
1997 (as amended) have incidental registration rights in such registration (the
shares requested to be registered pursuant to such agreement, the "Additional
Shares") and shall use its best efforts to register under the Securities Act,
for public sale in accordance with the method of disposition specified in the
notice from the Investors, the number of shares of Restricted Stock specified in
such notice (and in any notices received from other holders of Restricted Stock
within 20 days after their receipt of such notice from the Company) and any
Additional Shares which the Company is notified of within 20 days of the Company
Notice.  The Company shall be entitled to include in any registration statement
referred to in this Section 2 shares of Common Stock to be sold by the Company
for its own account.  Notwithstanding the foregoing, if the proposed method of
disposition specified by the Investors shall be an underwritten public offering,
the number of shares of Restricted Stock and Additional Shares (if any) to be
included in such an offering will be reduced, first by the Company with respect
to shares it wishes to register in such registration (if such registration is
the first demand registration requested by the holders of the Restricted Stock
or Additional Shares, if any) and then pro rata among the requesting holders of
                                       --------
Restricted Stock and Additional Shares (if any), based on the total number of
shares of Restricted Stock and Additional Shares (if any) so requested to be
registered, if and to the extent that the managing underwriter shall be of the
opinion that such inclusion would adversely affect the marketing of the
Restricted Stock and Additional Shares (if any) to be sold.  Notwithstanding the
foregoing, the first registration of shares pursuant to Section 2(a) above shall
not include any Additional Shares without the approval of the holders of a
majority of the then-outstanding Series C Preferred Stock, Series D

                                       2
<PAGE>

Preferred Stock, Series E Preferred Stock and Series F Preferred Stock on an as
converted basis. If such method of disposition shall be an underwritten public
offering, a majority of the holders of the Restricted Shares may designate the
managing underwriter of such offering. Notwithstanding the foregoing, the
Company shall be cut back pro rata with the holders of the Restricted Stock and
Additional Shares (if any), if the Company has successfully effected one demand
registration for holders of the Restricted Stock.

          (c) The Company shall not be required to effect more than two
registrations pursuant to Section 2(a) above.  In addition, the Company shall
not be obligated to effect any such registration, qualification or compliance
pursuant to this Agreement or the 1997 Registration Rights Agreement more than
once in any six (6) month period.  Subject to the foregoing, the Company shall
file a registration statement covering the Restricted Stock so requested to be
registered as soon as practicable after receipt of the request or requests of
the holders of the Restricted Stock.  Anything to the contrary in this Section 2
notwithstanding, a registration shall not be effected pursuant to this Section 2
with respect to any Restricted Stock once such Restricted Stock other wise may
be sold to the public without restriction.

          (d) Notwithstanding anything to the contrary contained in this Section
2, in the event that there is a firm commitment underwritten public offering of
securities of the Company pursuant to a registration statement covering
Restricted Stock and a holder of Restricted Stock does not elect to sell his
Restricted Stock to the underwriters of the Company's securities in connection
with such offering or elects to sell only a portion of its Restricted Stock to
the underwriters in connection with such offering, such holder shall agree to
refrain from selling or otherwise transferring its Restricted Stock or portion
thereof as the case may be for a period, to be determined by the managing
underwriter of the offering, of up to 180 days provided that the Company's
shares and any cut-back shares are subject to the same lock-up period.

          3.  Form S-3 Registration.
              ---------------------

          (a) At the time that the Company is qualified to use a Form S-3 (or
successor short form registration form, if applicable) for registration for
shares of its own stock or for shares of its stockholders and if the Company
shall receive from any holder or holders of Restricted Stock a written request
or requests that the Company effect a registration on Form S-3 and any related
qualification or compliance with respect to Restricted Stock owned by such
holder or holders, the Company will:

          (i) promptly give written notice of the proposed registration, and any
     related qualification or compliance, to all other holders of Restricted
     Stock; and

          (ii) as soon as practicable, effect such registration (including,
     without limitation, the execution of an undertaking to file post-effective
     amendments, appropriate qualifications under applicable blue sky or other
     state securities laws and appropriate compliance with applicable
     regulations issued under the Securities Act and any other government
     requirements or regulations) as may be so requested and as would permit or
     facilitate the sale and distribution of all or such portion of such
     holder's or holders'

                                       3
<PAGE>

     Restricted Stock as are specified in such request, together with all or
     such portion of the Restricted Stock of any holder or holders joining in
     such request as are specified in a written request given within thirty (30)
     days after receipt of such written notice from the Company, provided that
     (i) the Company may defer such registration for one period of up to 90 days
     during any 12-month period and (ii) the Company shall not be obligated to
     effect any such registration, qualification or compliance pursuant to this
     Agreement (A) more than once in any twelve month period, or (B) if the
     Company is not entitled to use Form S-3 for registration for shares of its
     own stock or for shares of its stockholders. Subject to the foregoing, the
     Company shall file a registration statement covering the Restricted Stock
     so requested to be registered as soon as practicable after receipt of the
     request or requests of the holders of the Restricted Stock.

          (b)  Registrations effected pursuant to this Section 3 shall not be
counted as requests for registration effected pursuant to Section 2.

          (c)  Anything to the contrary in this Section 3 notwithstanding, a
registration shall not be effected pursuant to this Section 3 (i) for Restricted
Stock with an aggregate market value of less than $2,000,000, or (ii) once the
Restricted Stock otherwise may be sold to the public without restriction.

          (d)  Notwithstanding anything to the contrary contained in this
Section 3, in the event that there is a firm commitment underwritten public
offering of securities of the Company pursuant to a registration covering
Restricted Stock and a holder of Restricted Stock does not elect to sell his
Restricted Stock to the underwriters of the Company's securities in connection
with such offering, such holder shall agree to refrain from selling or otherwise
transferring its Restricted Stock for a period, to be determined by the managing
underwriter that such sale would adversely effect the marketing of the
securities of the Company, of up to 180 days.

          4.  Incidental Registration.  If the Company at any time (other than
              -----------------------
pursuant to Section 2 hereof) proposes to register any of its Common Stock under
the Securities Act for sale to the public, whether for its own account or for
the account of other securityholders or both (except with respect to
registration statements on Form S-4 or S-8 or another form not available for
registering the Restricted Stock for sale to the public), it will give written
notice at such time to all holders of outstanding Restricted Stock of its
intention to do so.  Upon the written request of any such holder, given within
30 days after receipt of any such notice by the Company, to register any of its
Restricted Stock (which request shall state the intended method of disposition
thereof), the Company will use its best efforts to cause the Restricted Stock as
to which registration shall have been so requested to be included in the
securities to be covered by the registration statement proposed to be filed by
the Company, all to the extent requisite to permit the sale or other disposition
by the holder (in accordance with its written request) of such Restricted Stock
so registered; provided that nothing herein shall prevent the Company from
               --------
abandoning or delaying such registration at any time.  In the event that any
registration pursuant to this Section 4 shall be, in whole or in part, an
underwritten public offering of Common Stock, any request by a holder pursuant
to this Section 4 to register Restricted Stock shall specify that either (i)
such Restricted Stock is to be included in the underwriting on the same terms
and

                                       4
<PAGE>

conditions as the shares of Common Stock otherwise being sold through
underwriters under such registration or (ii) such Restricted Stock is to be sold
in the open market without any underwriting.  The number of shares of Restricted
Stock to be included in such an underwriting may be reduced (pro rata among the
                                                             --- ----
re questing holders of Restricted Stock and other requesting securityholders who
request pursuant to their demand or incidental registration rights or other
similar rights, based upon the total number of shares so requested to be
registered) if and to the extent that the managing underwriter shall be of the
opinion that such inclusion would adversely affect the marketing of the
securities to be sold by the Company therein.

          Notwithstanding anything to the contrary contained in this Section 4,
in the event that there is a firm commitment underwritten public offering of
securities of the Company pursuant to a registration covering Restricted Stock
and a holder of Restricted Stock does not elect to sell his Restricted Stock to
the underwriters of the Company's securities in connection with such offering,
such holder shall agree to refrain from selling or otherwise transferring its
Restricted Stock for a period, to be determined by the managing underwriter, of
up to 180 days.

          5.  Registration Procedures and Expenses.  If and whenever the Company
              ------------------------------------
is required by the provisions of Sections 2, 3 and 4 to use its best efforts to
effect the registration of any of the Restricted Stock under the Securities Act,
the Company will, as expeditiously as possible:

          (a) prepare (and afford counsel for the selling holders reasonable
     opportunity to review and comment thereon) and file with the Commission a
     registration statement (which, in the case of an underwritten public
     offering pursuant to Section 2 hereof, shall be on a form of general
     applicability satisfactory to the managing underwriter selected as therein
     provided) with respect to such securities and use its best efforts to cause
     such registration statement to become and remain effective for the period
     of the distribution contemplated thereby (deter mined as herein after
     provided);

          (b) prepare (and afford counsel for the selling holders reasonable
     opportunity to review and comment thereon)  and file with the Commission
     such amendments and supplements to such registration statement and the
     prospectus used in connection therewith as may be necessary to keep such
     registration statement effective for the period specified in paragraph (a)
     above and as comply with the provisions of the Securities Act with respect
     to the disposition of all Restricted Stock covered by such registration
     statement in accordance with the sellers' intended method of disposition
     set forth in such registration statement for such period;

          (c) furnish to each seller and to each underwriter such number of
     copies of the registration statement and the prospectus included therein
     (including each preliminary prospectus) as such persons may reasonably
     request in order to facilitate the public sale or other disposition of the
     Restricted Stock covered by such registration statement;

          (d) use its best efforts to register or qualify the Restricted Stock
     covered by such registration statement under the securities or blue sky
     laws of such jurisdictions as

                                       5
<PAGE>

     the sellers of Restricted Stock or, in the case of an underwritten public
     offering, the managing underwriter, shall reasonably request (provided that
     the Company will not be required to (i) qualify generally to do business in
     any jurisdiction where it would not otherwise be required to qualify but
     for this paragraph (d), (ii) subject itself to taxation in any such
     jurisdiction or (iii) consent to general service of process in any
     jurisdiction);

          (e) immediately notify each seller under such registration statement
     and each underwriter, at any time when a prospectus relating thereto is
     required to be delivered under the Securities Act, of the happening of any
     event as a result of which the prospectus contained in such registration
     statement, as then in effect, includes an untrue statement of a material
     fact or omits to state any material fact required to be stated therein or
     necessary to make the statements therein not misleading in the light of the
     circumstances then existing;

          (f) use its best efforts (if the offering is underwritten) to furnish,
     at the request of any underwriter, on the date that Restricted Stock is
     delivered to the underwriters for sale pursuant to such registration:  (i)
     an opinion dated such date of counsel representing the Company for the
     purposes of such registration, addressed to the underwriters, stating that
     such registration statement has become effective under the Securities Act
     and that (A) to the best knowledge of such counsel, no stop order
     suspending the effectiveness thereof has been issued and no proceedings for
     that purpose have been instituted or are pending or contemplated under the
     Securities Act, (B) the registration statement, the related prospectus, and
     each amendment or supplement thereof, comply as to form in all material
     respects with the requirements of the Securities Act and the applicable
     rules and regulations of the Commission thereunder (except that such
     counsel need express no opinion as to financial statements, the notes
     thereto, and the financial schedules and other financial and statistical
     data contained therein) and (C) to such other effects as may reasonably be
     requested by counsel for the underwriters or by such seller or its counsel,
     and (ii) a letter dated such date from the independent public accountants
     retained by the Company, addressed to the underwriters, stating that they
     are independent public accountants within the meaning of the Securities Act
     and that, in the opinion of such accountants, the financial statements of
     the Company included in the registration statement or the prospectus, or
     any amendment or supplement thereof, comply as to form in all material
     respects with the applicable accounting requirements of the Securities Act,
     and such letter shall additionally cover such other financial matters
     (including information as to the period ending no more than five business
     days prior to the date of such letter) with respect to the registration in
     respect of which such letter is being given as such underwriters or seller
     may reasonably request; and

          (g) during normal business hours and with reasonable notice, make
     available for inspection by each seller, any underwriter participating in
     any distribution pursuant to such registration statement, and any attorney,
     accountant or other agent retained by such seller or underwriter, all
     financial and other records, pertinent corporate documents and properties
     of the Company, and cause the Company's officers, directors and employees
     to supply all information reasonably requested by any such seller,
     underwriter, attorney,

                                       6
<PAGE>

     accountant or agent in connection with such registration statement and
     permit such seller, attorney, accountant or agent to participate in the
     preparation of such registration statement.

For purposes of paragraphs (a) and (b) above, the period of distribution of
Restricted Stock in a firm commitment underwritten public offering shall be
deemed to extend until each underwriter has completed the distribution of all
securities purchased by it, and the period of distribution of Restricted Stock
in any other registration shall be deemed to extend until the earlier of the
sale of all Restricted Stock covered thereby or six months after the effective
date thereof.

          In connection with each registration hereunder, the selling holders of
Restricted Stock will furnish to the Company in writing such information with
respect to themselves and the proposed distribution by them as shall be
reasonably necessary in order to assure compliance with federal and applicable
state securities laws.

          In connection with each registration pursuant to Sections 2, 3 and 4
hereof covering an underwritten public offering, the Company agrees to enter
into a written agreement with the managing underwriter selected in the manner
herein provided in such form and containing such provisions as are customary in
the securities business for such an arrangement between major underwriters and
companies of the Company's size and investment stature, provided, however, that
                                                        --------  -------
such agreement shall not contain any such provision applicable to the Company
which is inconsistent with the provisions hereof and provided, further, however,
                                                     --------  -------  -------
that the time and place of the closing under said agreement shall be as mutually
agreed upon among the Company and such managing underwriter.

          Notwithstanding anything to the contrary contained herein, the Company
shall not be required to include any class of securities in a registration
statement other than Common Stock.

          6.  Expenses.  All expenses incurred by the Company in complying with
              --------
Sections 2, 3 and 4 hereof, including, without limitation, all registration and
filing fees, printing expenses, fees and disbursements of counsel and
independent public accountants for the Company, fees of the National Association
of Securities Dealers, Inc., transfer taxes, fees of transfer agents and
registrars and fees, but excluding any Selling Expenses, are herein called
"Registration Expenses".  All underwriting discounts and selling commissions
applicable to the sale of Restricted Stock and fees and expenses of counsel for
the sellers of Restricted Stock are herein called "Selling Expenses".

The Company will pay all Registration Expenses in connection with each
registration statement filed pursuant to Sections 2, 3 and 4 hereof.

          7.  Indemnification.  In the event of a registration of any of the
              ---------------
Restricted Stock under the Securities Act pursuant to Sections 2, 3 and 4
hereof, the Company will indemnify and hold harmless each seller of such
Restricted Stock thereunder and each underwriter of Restricted Stock thereunder
and each other person, if any, who controls such

                                       7
<PAGE>

seller or underwriter within the meaning of the Securities Act, against any
losses, claims, damages or liabilities, joint or several, to which such seller
or underwriter or controlling person may become subject under the Securities Act
or otherwise, insofar as such losses, claims, damages or liabilities (or actions
in respect thereof) arise out of or are based upon any untrue statement or
alleged untrue statement of any material fact contained in any registration
statement under which such Restricted Stock was registered under the Securities
Act pursuant to Sections 2, 3 and 4 hereof, any preliminary prospectus or final
prospectus contained therein, or any amendment or supplement thereof, or arise
out of or are based upon the 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 each such seller, each such
underwriter and each such controlling person for any legal or other expenses
reasonably incurred by them in connection with investigating or defending any
such loss, claim, damage, liability or action; provided, however, that the
                                               --------  -------
Company will not be liable in any such case if and to the extent that any such
loss, claim, damage or liability arises out of or is based upon an untrue
statement or alleged untrue statement or omission or alleged omission so made in
conformity with information furnished by such seller, such underwriter or such
controlling person in writing specifically for use in such registration
statement or prospectus.

          In the event of a registration of any of the Restricted Stock under
the Securities Act pursuant to Sections 2, 3 or 4 hereof, each seller of such
Restricted Stock thereunder, severally and not jointly, will indemnify and hold
harmless the Company and each person, if any, who controls the Company within
the meaning of the Securities Act, each officer of the Company who signs the
registration statement, each director of the Company, each underwriter and each
person who controls any underwriter within the meaning of the Securities Act,
against all losses, claims, damages or liabilities, joint or several, to which
the Company or such officer or director or underwriter or controlling person may
become subject under the Securities Act or otherwise, insofar as such losses,
claims, damages or liabilities (or actions in respect thereof) arise out of or
are based upon any untrue statement or alleged untrue statement of any material
fact contained in the registration statement under which such Restricted Stock
was registered under the Securities Act pursuant to Sections 2, 3 or 4, any
preliminary prospectus or final prospectus contained therein, or any amendment
or supplement thereof, or arise out of or are based upon the 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 and each such officer, director, underwriter and controlling person for
any legal or other expenses reasonably incurred by them in connection with
investigating or defending any such loss, claim, damage, liability or action;
provided, however, that such seller will be liable hereunder in any such case if
--------  -------
and only to the extent that any such loss, claim, damage or liability arises out
of or is based upon an untrue statement or alleged untrue statement or omission
or alleged omission made in reliance upon and in conformity with information
pertaining to such seller, as such, furnished in writing to the Company by such
seller specifically for use in such registration statement or prospectus;
provided, further, however, that the liability of each seller hereunder shall be
--------  -------  -------
limited to the proportion of any such loss, claim, damage, liability or expense
which is equal to the proportion that the public offering price of shares sold
by such seller under such registration statement bears to the total public
offering price of all securities sold

                                       8
<PAGE>

thereunder, but not to exceed the proceeds (net of underwriting discounts and
commissions) received by such seller from the sale of Restricted Stock covered
by such registration statement.

          Promptly after receipt by an indemnified party hereunder of notice of
the commencement of any action, such indemnified party shall, if a claim in
respect thereof is to be made against the indemnifying party hereunder, notify
the indemnifying party in writing thereof, but the omission so to notify the
indemnifying party shall not relieve it from any liability which it may have to
any indemnified party other than under this Section 7.  In case any such action
shall be brought against any indemnified party and it shall notify the
indemnifying party of the commencement thereof, the indemnifying party shall be
entitled to participate in and, to the extent it shall wish, to assume and
undertake the defense thereof with counsel satisfactory to such indemnified
party, and, after notice from the indemnifying party to such indemnified party
of its election so to assume and undertake the defense thereof, the indemnifying
party shall not be liable to such indemnified party under this Section 7 for any
legal expenses subsequently incurred by such indemnified party in connection
with the defense thereof other than reasonable costs of investigation and of
liaison with counsel so selected; provided, however, that, if the defendants in
                                  --------  -------
any such action include both the indemnified party and the indemnifying party
and the indemnified party shall have reasonably concluded that there may be
reasonable defenses available to it which are different from or additional to
those available to the indemnifying party, or if the interests of the
indemnified party reasonably may be deemed to conflict with the interests of the
indemnifying party, the indemnified party shall have the right to select a
separate counsel and to assume such legal defenses and otherwise to participate
in the defense of such action, with the expenses and fees of such separate
counsel and other expenses related to such participation to be reimbursed by the
indemnifying party as incurred.

          Notwithstanding the foregoing, any indemnified party shall have the
right to retain its own counsel in any such action, but the fees and
disbursements of such counsel shall be at the expense of such indemnified party
unless (i) the indemnifying party shall have failed to retain counsel for the
indemnified person as aforesaid or (ii) the indemnifying party and such
indemnified party shall have mutually agreed to the retention of such counsel.
It is understood that the indemnifying party shall not, in connection with any
action or related actions in the same jurisdiction, be liable for the fees and
disbursements of more than one separate firm qualified in such jurisdiction to
act as counsel for the indemnified party.  The indemnifying party shall not be
liable for any settlement of any proceeding effected without its written
consent, but if settled with such consent or if there be a final judgment for
the plaintiff, the indemnifying party agrees to indemnify the indemnified party
from and against any loss or liability by reason of such settlement or judgment.

          If the indemnification provided for in the first two paragraphs of
this Section 7 is unavailable or insufficient to hold harmless an indemnified
party under such paragraphs in respect of any losses, claims, damages or
liabilities or actions in respect thereof referred to therein, then each
indemnifying party shall in lieu of indemnifying such indemnified party con
tribute to the amount paid or payable by such indemnified party as a result of
such losses, claims, damages, liabilities or actions in such proportion as
appropriate to reflect the relative fault of the Company, on the one hand, and
the underwriters and the sellers of such Restricted Stock, on the

                                       9
<PAGE>

other, in connection with the statements or omissions which resulted in such
losses, claims, damages, liabilities or actions as well as any other relevant
equitable considerations, including the failure to give any notice under the
third paragraph of this Section 7. The relative fault shall be determined by
reference to, among other things, whether the untrue or alleged untrue statement
of a material fact relates to information supplied by the Company, on the one
hand, or the underwriters and the sellers of such Restricted Stock, on the
other, and to the parties' relative intent, knowledge, access to information and
opportunity to correct or prevent such statement or omission. The Company and
each of you agree that it would not be just and equitable if contributions
pursuant to this paragraph were determined by pro rata allocation (even if all
                                              --- ----
of the sellers of such Restricted Stock were treated as one entity for such
purpose) or by any other method of allocation which did not take account of the
equitable considerations referred to above in this paragraph.  The amount paid
or payable by an indemnified party as a result of the losses, claims, damages,
liabilities or action in respect thereof, referred to above in this paragraph,
shall be deemed to include any legal or other expenses reasonably incurred by
such indemnified party in connection with investigating or defending any such
action or claim.  Notwithstanding the provisions of this paragraph, the sellers
of such Restricted Stock shall not be required to contribute any amount in
excess of the amount, if any, by which the total price at which the Common Stock
sold by each of them was offered to the public exceeds the amount of any damages
which they would have otherwise been required to pay by reason of such untrue or
alleged untrue statement or omission.  No person guilty of fraudulent
misrepresentations (within the meaning of Section 11(f) of the Securities Act),
shall be entitled to contribution from any person who is not guilty of such
fraudulent misrepresentation.

          The indemnification of underwriters provided for in this Section 7
shall be on such other terms and conditions as are at the time customary and
reasonably required by such underwriters.  In that event the indemnification of
the sellers of Restricted Stock in such underwriting shall at the sellers'
request be modified to conform to such terms and conditions.

          8.  Changes in Common Stock.  If, and as often as, there are any
              -----------------------
changes in the Common Stock by way of stock split, stock dividend, combination
or reclassification, or through merger, consolidation, reorganization or
recapitalization, or by any other means, appropriate adjustment shall be made in
the provisions hereof, as may be required, so that the rights and privileges
granted hereby shall continue with respect to the Common Stock as so changed.

          9.  Representations and Warranties of the Company.  The Company
              ---------------------------------------------
represents and warrants to you as follows:

          (a) The execution, delivery and performance of this Agreement by the
     Company have been duly authorized by all requisite corporate action and
     will not violate any provision of law, any order of any court or other
     agency of government, the Certificate of Incorporation as amended or By-
     laws as amended of the Company, or any provision of any indenture,
     agreement or other instrument to which it or any of its properties or
     assets is bound, or conflict with, result in a breach of or constitute
     (with due notice or lapse of time or both) a default under any such
     indenture, agreement or other

                                       10
<PAGE>

     instrument, or result in the creation or imposition of any lien, charge or
     encumbrance of any nature whatsoever upon any of the properties or assets
     of the Company.

          (b) This Agreement has been duly executed and delivered by the Company
     and constitutes the legal, valid and binding obligation of the Company,
     enforceable in accordance with its terms, subject to considerations of
     public policy in the case of the indemnification provisions hereof.

          10.  Rule 144 Reporting.  The Company agrees with you as follows:
               ------------------

          (a) The Company shall make and keep public information available, as
     those terms are understood and defined in Rule 144 under the Securities
     Act, at all times from and after the date it is first required to do so.

          (b) The Company shall file with the Commission in a timely manner all
     reports and other documents as the Commission may prescribe under Section
     13(a) or 15(d) of the Exchange Act at any time after the Company has become
     subject to such reporting requirements of the Exchange Act.

          (c) The Company shall furnish to such holder of Restricted Stock
     forthwith upon request (i) a written statement by the Company as to its
     compliance with the reporting requirements of Rule 144 (at any time from
     and after the date it first becomes subject to such reporting requirements,
     and of the Securities Act and the Exchange Act (at any time after it has
     become subject to such reporting requirements), (ii) a copy of the most
     recent annual or quarterly report of the Company, and (iii) such other
     reports and documents so filed as a holder may reasonably request to avail
     itself of any rule or regulation of the Commission allowing a holder of
     Restricted Stock to sell any such securities without registration.

          11.  Miscellaneous.
               -------------

          (a) All covenants and agreements contained in this Agreement by or on
     behalf of any of the parties hereto shall bind and inure to the benefit of
     the respective successors and assigns of the parties hereto whether so
     expressed or not.  Without limiting the generality of the foregoing, the
     registration rights conferred herein on the holders of Restricted Stock
     shall inure to the benefit of any and all subsequent holders from time to
     time of the Restricted Stock.

          (b) All notices, requests, consents and other communications hereunder
     shall be in writing and shall be mailed by first class registered mail,
     postage prepaid, addressed as follows:

          if to the Company, to it at 1372 Broadway, 12A, New York, New York
     10018, Attn:  President;

                                       11
<PAGE>

          if to any of the Investors, to him or it at his or its address listed
     in the Company's records;

          if to any subsequent holder of Restricted Stock, to it at such address
     as may have been furnished to the Company in writing by such holder;

     or, in any case, at such other address or addresses as shall have been
     furnished in writing to the Company (in the case of a holder of Restricted
     Stock) or to the holders of Restricted Stock (in the case of the Company).

          (c) This Agreement shall be governed by and construed in accordance
     with the laws of the State of New York, without giving effect to the
     principles of conflict of laws thereof.

          (d) This Agreement constitutes the entire agreement of the parties
     with respect to the subject matter hereof and may not be modified or
     amended except in writing signed by the Company and the holders of not less
     than two-thirds in interest of the holders of Restricted Stock then out
     standing; provided that any such amendment which would adversely affect the
     rights of any holder(s) of Restricted Stock must also be approved in
     writing by holder(s) who would be so adversely affected.

          (e) This Agreement may be executed in two or more counter parts, each
     of which shall be deemed an original, but all of which together shall
     constitute one and the same instrument.

                                       12
<PAGE>

               [Signature Page to Registration Rights Agreement]

          Please indicate your acceptance of the foregoing by signing and
returning the enclosed counterpart of this Agreement, whereupon this Agreement
shall be a binding agreement between the Company and you.

                              Very truly yours,

                              INTRALINKS, INC.

                              By: _______________________________
                                  Name:
                                  Title:

AGREED TO AND ACCEPTED as of the date first above written:

__________________________________     Number of Shares of Series F
SERIES F INVESTOR:                     Convertible Preferred Stock:

                                       _______________________
By: ___________________________
    Name:
    Title:

                               SERIES E INVESTOR:

JOHNSON & JOHNSON DEVELOPMENT CORPORATION

By: ____________________
    Name:
    Title:

REUTERS HOLDINGS SWITZERLAND S.A.

By: ____________________
    Name:
    Title:
<PAGE>

               [Signature Page to Registration Rights Agreement]

________________________
Younes Nazarian

DAVID & ANGELLA NAZARIAN FAMILY TRUST

By: ____________________
    Name:
    Title:

SAM NAZARIAN TRUST

By: ____________________
    Name:
    Title:

SHARON NAZARIAN BARADARAN TRUST

By: ____________________
    Name:
    Title:
<PAGE>

               [Signature Page to Registration Rights Agreement]

                               SERIES D INVESTOR:

Ernst & Young U.S. LLP

By: ___________________________
    Name:
    Title:

                              SERIES C INVESTORS:

Euclid Partners IV, L.P.

By: ____________________
    Name:
    Title:

Perseus Capital, LLC

By: ____________________
    Name:
    Title:

Catalyst Investments (Belgium) NV)

By: ____________________
    Name:
    Title:

Sculley Brothers LLC

By: ____________________
    Name:
    Title:
<PAGE>

               [Signature Page to Registration Rights Agreement]

____________________
Duncan W. Brown

EUGENE A. TOMEI LIVING TRUST

By: ____________________
    Name:
    Title:

P/A FUND III, L.P.

By: APA Pennsylvania Partners III, L.P.
    its General Partner
    By:  Patricof & Co. Managers, Inc.
         its General Partner

By: ____________________
    Name:
    Title:

PATRICOF PRIVATE INVESTMENT CLUB II, L.P.

By: APA Excelsior V Partners, L.P.,
    P.A. Fund III, L.P., its General Partner
    By:  Patricof & Co. Managers, Inc.
         its General Partner

By: ____________________
    Name:
    Title:

<PAGE>

           [Signature Page to Registration Rights Agreement]

APA EXCELSIOR V, L.P.

By: APA Excelsior V Partners, L.P.
    its General Partner
    By:  Patricof & Co. Managers, Inc.
         its General Partner

By: ____________________
    Name:
    Title:

Smart Technology Ventures, LLC

By: ____________________
    Name:
    Title:

Rita Angel, IRA

By: ____________________
    Name:
    Title:

New York Small Business Venture Fund, LLC

By: ____________________
    Name:
    Title:

Solar Group

By: ____________________
    Name:
    Title:
<PAGE>

               [Signature Page to Registration Rights Agreement]

Hull Overseas, Ltd.

By: ____________________
    Name:
    Title:

Joshua Angel, IRA

By: ____________________
    Name:
    Title:

C.E. Unterberg, Towbin LLC

By: ____________________
    Name:
    Title:

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