<PAGE>

                                                                   EXHIBIT 10.27

                                                               [Second Tranche]



          NEITHER THESE WARRANTS NOR THE SHARES UNDERLYING THESE WARRANTS HAVE
          BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933 OR THE LAWS OF ANY
          STATE. THEY MAY NOT BE SOLD OR OTHERWISE TRANSFERRED UNLESS THEY ARE
          REGISTERED UNDER SUCH ACT AND APPLICABLE STATE SECURITIES LAWS IF
          NECESSARY, OR AN EXEMPTION FROM REGISTRATION IS AVAILABLE. THESE
          WARRANTS AND THE SHARES UNDERLYING THESE WARRANTS ARE ALSO SUBJECT TO
          ADDITIONAL RESTRICTIONS ON TRANSFER AND OTHER PROVISIONS SET FORTH IN
          THAT CERTAIN AMENDED AND RESTATED SHAREHOLDERS' AGREEMENT, A COPY OF
          WHICH MAY BE OBTAINED FROM INTRALINKS, INC.



76,923 Warrants                                               June 30, 1999

                              WARRANT CERTIFICATE

                               INTRALINKS, INC.

          This warrant certificate ("Warrant Certificate") certifies that for
value received R. W. Johnson Pharmaceutical Research Institute ("PRI") or
registered assigns (the "Holder") is the owner of the number of warrants (the
"Warrants") specified above, each of which entitles the Holder thereof to
purchase on or before the Expiration Date (as defined herein) one fully paid and
non-assessable share of Common Stock, $.01 par value, (the "Common Stock") of
IntraLinks, Inc. (the "Company"), for the Purchase Price (defined in Section 1
below) in lawful money of the United States of America (subject to adjustment as
hereinafter provided).  Upon the occurrence of an Exercise Event (as defined
herein), the Company may require the Holder to exercise immediately all of the
Warrants represented by this Warrant Certificate.

     1.   Warrant; Purchase Price
          -----------------------

     Each Warrant initially shall entitle the Holder to purchase one share of
Common Stock of the Company, and the purchase price payable upon exercise of the
Warrant (the "Purchase Price") shall initially be $13.00 per share of Common
Stock , subject to adjustment as hereinafter provided, unless otherwise provided
herein. The Purchase Price and number of shares of
<PAGE>

Common Stock issuable upon exercise of this Warrant are subject to adjustment as
provided in Section 5 hereof. The shares of Common Stock issuable upon exercise
of the Warrant (and/or other shares of stock so issuable by reason of any
adjustments pursuant to Section 5) are sometimes referred to herein as the
"Warrant Shares."

     2.   Exercise; Expiration Date; No Fractional Shares; Reservation of Shares
          ----------------------------------------------------------------------

     2.1. The Warrants are exercisable, at the option of the Holder, in whole or
in part on or before the Expiration Date, commencing on the earlier of (i) the
second anniversary of the date hereof and (ii) an Exercise Event, upon surrender
of this Warrant Certificate to the Company together with a duly completed Notice
of Exercise, in the form attached hereto as Exhibit A, and payment of the
                                            ---------
Purchase Price. In the case of exercise of less than the entire Warrant
represented by this Warrant Certificate, the Company shall cancel the Warrant
Certificate upon the surrender thereof and shall execute and deliver a new
Warrant Certificate for the balance of such Warrant. Notwithstanding any other
provision of this Warrant Certificate, upon the occurrence of an Exercise Event
at a price per share in excess of the Purchase Price, the Company may, at its
sole option, require the Holder to immediately exercise all (but not less than
all) of the Warrants represented by this Warrant Certificate in exchange for
payment of the Purchase Price. The term "Exercise Event" shall mean the
completion of a firm commitment initial public offering of the Company's common
stock or the sale of any shares of the Company owned by Johnson & Johnson
Development Corporation or its permitted assigns as a result of and pursuant to
Section 4.1(c) of that certain Amended and Restated Shareholders' Agreement of
even date herewith by and among the Company and its Shareholders.

     2.2. The term "Expiration Date" shall mean the earlier of (i) 5:00 p.m.
New York time thirty months from the date hereof, or if such day shall in the
State of New York be a holiday or a day on which banks are authorized to close,
then 5:00 p.m. New York time the next following day which in the State of New
York is not a holiday or a day on which banks are authorized to close or (ii)
the time that PRI (A) terminates the Collaboration and Service Agreement between
PRI and the Company of even date prior to payment of the second $250,000 payment
described in Article 3 thereof, (B) refuses to collaborate on IntraTrials or (C)
(after the acceptance of IntraTrials) refuses to use IntraTrials.

     2.3. No fractional shares shall be issued upon exercise or conversion (in
whole or in part) of the Warrants and the number of shares of Common Stock to be
issued shall be rounded down to the nearest whole share, and there shall be no
payment to the Holder for any such rounded fractional shares.

     2.4. The Company covenants that it will at all times reserve and keep
available out of its authorized capital stock, solely for the purpose of issue
upon exercise of the Warrants, such number of shares of Common Stock as shall
then be issuable upon the exercise of all outstanding Warrants. The Company
covenants that all shares of Common Stock which shall be issuable upon exercise
of the Warrants shall, upon issuance in accordance with the terms hereof, be
duly and validly issued and fully paid and non-assessable and free from all
taxes, liens, encumbrances

                                       2
<PAGE>

and charges with respect to the issue thereof, and that upon issuance the
Company shall use its commercially reasonable efforts to cause such shares to be
listed on each national securities exchange, if any, on which the other shares
of such outstanding capital stock of the Company are then listed.

     3.    Registration and Transfer on Company Books
           ------------------------------------------

     3.1.  The Company shall maintain books for the registration and transfer of
the Warrants and the registration and transfer of the Warrant Shares.

     3.2.  Prior to due presentment for registration of transfer of this Warrant
Certificate, or the Warrant Shares, the Company may deem and treat the
registered Holder as the absolute owner thereof.

     3.3.  The Warrants shall be freely assignable by PRI to any affiliate of
PRI, provided that such affiliate, prior to the assignment by PRI, represents to
the Company that it is purchasing the Warrants for investment purposes only and
not with a view of or towards subsequent transfer (except to an affiliate) or
resale and that such sale or transfer is permitted under the securities laws.

     4.    Loss or Mutilation
           ------------------

     Upon receipt by the Company of reasonable evidence of the ownership of and
the loss, theft, destruction or mutilation of any Warrant Certificate and, in
the case of loss, theft or destruction, of indemnity reasonably satisfactory to
the Company, or, in the case of mutilation, upon surrender and cancellation of
the mutilated Warrant Certificate, the Company shall execute and deliver in lieu
thereof a new Warrant Certificate representing an equal number of Warrant
Shares.

     5.    Adjustment of Purchase Price and Number of Shares
        Deliverable; Reorganizations and Recapitalizations
        --------------------------------------------------

     5.1.  The number of Warrant Shares purchasable upon the exercise of the
Warrants and the Purchase Price with respect to the Warrant Shares shall be
subject to adjustment as follows:

           (a)  In case the Company shall (i) declare a dividend or make a
distribution on its Common Stock payable in shares of its capital stock, (ii)
subdivide its outstanding shares of Common Stock through stock split or
otherwise, (iii) combine its outstanding shares of Common Stock into a smaller
number of shares of Common Stock, or (iv) issue by reclassification of its
Common Stock (including any reclassification in connection with a consolidation
or merger in which the Company is the continuing corporation) other securities
of the Company, the number and/or nature of Warrant Shares purchasable upon
exercise of the Warrants immediately prior thereto shall be adjusted so that the
Holder shall be entitled to receive the kind and number of Warrant Shares or
other securities of the Company which he or it would have owned or have been
entitled to receive after the happening of any of the events

                                       3
<PAGE>

described above, had such Warrants been exercised immediately prior to the
happening of such event or any record date with respect thereto. Any adjustment
made pursuant to this paragraph (a) shall become effective retroactively as of
the record date of such event.

           (b)  In the event of any capital reorganization or any
reclassification of the capital stock of the Company or in case of the
consolidation or merger of the Company with another corporation (other than a
consolidation or merger in which the outstanding shares of the Company's Common
Stock are not converted into or exchanged for other rights or interests), or in
the case of any sale, transfer or other disposition to another corporation of
all or substantially all the properties and assets of the Company, the Holder of
the Warrants shall thereafter be entitled to purchase (and it shall be a
condition to the consummation of any such reorganization, reclassification,
consolidation, merger, sale, transfer or other disposition that appropriate
provisions shall be made so that such Holder shall thereafter be entitled to
purchase) the kind and amount of shares of stock and other securities and
property (including cash) which the Holder would have been entitled to receive
had such Warrant been exercised immediately prior to the effective date of such
reorganization, reclassification, consolidation, merger, sale, transfer or other
disposition; and in any such case appropriate adjustments shall be made in the
application of the provisions of this Section 5 with respect to rights and
interest thereafter of the Holder of the Warrants to the end that the provisions
of this Section 5 shall thereafter be applicable, as near as reasonably may be,
in relation to any shares or other property thereafter purchasable upon the
exercise of the Warrants. The provisions of this Section 5.1(b) shall similarly
apply to successive reorganizations, reclassifications, consolidations, mergers,
sales, transfers or other dispositions.

           (c)  Whenever the number of Warrant Shares purchasable upon the
exercise of the Warrants is adjusted, as provided in this Section 5.1, the
Purchase Price with respect to the Warrant Shares shall be adjusted by
multiplying such Purchase Price immediately prior to such adjustment by a
fraction, of which the numerator shall be the number of Warrant Shares
purchasable upon the exercise of the Warrants immediately prior to such
adjustment, and of which the denominator shall be the number of Warrant Shares
so purchasable immediately thereafter.

     5.2.  Whenever the number of Warrant Shares purchasable upon the exercise
of the Warrant or the Purchase Price of such Warrant Shares is adjusted, as
herein provided, the Company shall mail to the Holder, at the address of the
Holder shown on the books of the Company, a notice of such adjustment or
adjustments, prepared and signed by the Chief Financial Officer or Secretary of
the Company, which sets forth the number of Warrant Shares purchasable upon the
exercise of each Warrant and the Purchase Price of such Warrant Shares after
such adjustment, a brief statement of the facts requiring such adjustment and
the computation by which such adjustment was made.

     5.3.  In the event that at any time prior to the expiration of the Warrants
and prior to their exercise:

                                       4
<PAGE>

          (a)  the Company shall offer for subscription to the holders of the
Common Stock any additional shares of stock of any class or any other securities
convertible into Common Stock or any rights to subscribe thereto; or

          (b)  the Company shall declare any stock split, stock dividend,
subdivision, combination, or similar distribution with respect to the Common
Stock, regardless of the effect of any such event on the outstanding number of
shares of Common Stock ; or

          (c)  the Company shall declare a dividend with respect to the Common
Stock, other than a dividend payable in shares of the Company's own Common
Stock; or

          (d)  there shall be a voluntary or involuntary dissolution,
liquidation, or winding up of the Company (other than in connection with a
consolidation, merger, or sale of all or substantially all of its property,
assets and business as an entity);

          (e)  there shall be any capital change in the Company as set forth in
Section 5.1(b);

(each such event hereinafter being referred to as a "Notification Event"), the
Company shall cause to be mailed to the Holder, not less than 10 days prior to
the record date, if any, in connection with such Notification Event (provided,
however, that if there is no record date, or if 10 days prior notice is
impracticable, as soon as practicable) written notice specifying the nature of
such event and the effective date of, or the date on which the books of the
Company shall close or a record shall be taken with respect to, such event.
Such notice shall also set forth facts indicating the effect of such action, if
any (to the extent such effect may be known at the date of such notice), on the
Purchase Price and the kind and amount of the shares of stock or other
securities or property deliverable upon exercise of the Warrant.

     6.   Voluntary Adjustment by the Company
          -----------------------------------

     The Company may, at its option, at any time during the term of the
Warrants, reduce the then current Purchase Price to any amount deemed
appropriate by the Board of Directors of the Company and/or extend the date of
the expiration of the Warrants.

     7.   Registration Rights
          -------------------

     The Warrant Shares shall have the registration rights set forth in the
Amended and Restated Registration Rights Agreement of even date herewith by and
among the Company, the Holder and the other securityholders of the Company named
therein.

     8.   Governing Law
          -------------

     This Warrant Certificate shall be governed by and construed in accordance
with the laws of the State of New York, without regard to the conflict of law
principles thereof.

                                       5
<PAGE>

          IN WITNESS WHEREOF, the Company has caused this Warrant Certificate to
be duly executed by its officers thereunto duly authorized and its corporate
seal to be affixed hereon, as of this 30/th/ day of June, 1999.


                              INTRALINKS, INC.



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

Attest:


_____________________________
Name:
Title:

                         SOLELY WITH RESPECT TO THE PENULTIMATE
                         SENTENCE OF SECTION 2.1 HEREOF

                         R.W. JOHNSON PHARMACEUTICAL RESEARCH
                         INSTITUTE

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

          IN WITNESS WHEREOF, the Company has caused this Warrant Certificate to
be duly executed by its officers thereunto duly authorized and its corporate
seal to be affixed hereon, as of this 30th day of June, 1999.


                              INTRALINKS, INC.



                              By:
                                   ___________________________
                                   Name:
                                   Title:

Attest:


_____________________________
Name:
Title:

                         SOLELY WITH RESPECT TO THE PENULTIMATE
                         SENTENCE OF SECTION 2.1 HEREOF

                         R.W. JOHNSON PHARMACEUTICAL RESEARCH
                         INSTITUTE

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

                                                                 EXHIBIT A

                              NOTICE OF EXERCISE


          The undersigned hereby irrevocably elects to exercise, pursuant to
Section 2 of the Warrant Certificate accompanying this Notice of Exercise,
____ ____ Warrants of the total number of Warrants owned by the undersigned
pursuant to the accompanying Warrant Certificate, and herewith makes payment of
the purchase price of such shares in full.


                              Name of Holder

                              ___________________________________
                              Signature


                              Address:

                              ___________________________________

                              __________________________________

                              __________________________________