<PAGE>
                                                                   Exhibit 10.48


                         REGISTRATION RIGHTS AGREEMENT

     This Agreement dated as of July 1, 1996 is entered into by and among
Biogen, Inc., a Massachusetts corporation (the "Purchaser") and Ontogeny, Inc.,
a Delaware corporation (the "Company").

     WHEREAS, the Company and the Purchasers desire to provide for certain
arrangements with respect to the registration of shares of capital stock of the
Company under the Securities Act of 1933;

     NOW, THEREFORE, in consideration of the mutual promises and covenants
contained in this Agreement, the parties hereto agree as follows:

     1. Registration Rights.

        1.1 Certain Definitions. As used in this Agreement, the following terms
shall have the following respective meanings:

        "Commission" means the Securities and Exchange Commission, or any
other Federal agency at the time administering the Securities Act.

        "Common Stock" means the common stock, $.01 par value per share,
of the Company.

        "Exchange Act" means the Securities Exchange Act of 1934, as amended,
or any similar Federal statute, and the rules and regulations of the Commission
issued under such Act, as they each may, from time to time, be in effect.

         "Registration Statement" means a registration statement filed by the
Company with the Commission for a public offering and sale of Common Stock
(other than a registration statement on Form S-8 or Form S-4, or their
successors, or any other form for a similar limited purpose, any registration
statement covering only securities proposed to be issued in exchange for
securities or assets of another corporation or any registration statement
covering only securities to be sold for the account of stockholders of the
Company).

         "Registration Expenses" means the expenses described in Section 1.5.

         "Registrable Shares" means (i) the shares of Common Stock issued or
issuable upon conversion of the Shares, (ii) any other shares of Common Stock
issued in respect of such shares (because of stock splits, stock dividends,
reclassifications, recapitalizations, or similar events); provided, however,
that shares of Common Stock which are Registrable Shares shall cease to be
Registrable Shares (i) upon any sale pursuant to a Registration Statement or
Rule 144 under the Securities Act or (ii) upon any sale in any manner to a
person or entity which, by virtue of Section 2 of this Agreement, is not
entitled to the rights provided by this Agreement.  Wherever reference is made
in this Agreement to a request or consent of holders of a certain percentage of
Registrable Shares, the determination of such percentage shall include shares of
Common Stock issuable upon conversion of the Shares even if such conversion has
not yet been effected.
<PAGE>

         "Securities Act" means the Securities Act of 1933, as amended, or any
similar Federal statute, and the rules and regulations of the Commission issued
under such Act, as they each may, from time to time, be in effect.

         "Shares" means (1) the shares of Series C Convertible Preferred Stock
issued pursuant to the Series C Preferred Stock Purchase Agreement of even date
herewith by and between the Company and the Purchaser.

         "Stockholders" means the Purchaser and any persons or entities to whom
the rights granted under this Agreement are transferred by Purchaser, pursuant
to Section 2 hereof.

        1.2  Required Registrations.

             (a) At any time after the Company becomes eligible to file a
     Registration Statement on Form S-3 (or any successor form relating to
     secondary offerings), a Stockholder or Stockholders may request the
     Company, in writing, to effect the registration on Form S-3 (or such
     successor form), of Registrable Shares having an aggregate offering price
     of at least $1,000,000 (based on the then current public market price).
     Upon receipt of any such request, the Company shall promptly give written
     notice of such proposed registration to all Stockholders. Such Stockholders
     shall have the right, by giving written notice to the Company within 30
     days after the Company provides its notice, to elect to have included in
     such registration such of their Registrable Shares as such Stockholders may
     request in such notice of election; provided that if the underwriter (if
     any) managing the offering determines that, because of marketing factors,
     all of the Registrable Shares requested to be registered by all
     Stockholders may not be included in the offering, then all Stockholders who
     have requested registration shall participate in the registration pro rata
     based upon their total ownership of shares of Common Stock (giving effect
     to the conversion into Common Stock of all securities convertible
     thereinto). Thereupon, the Company shall, as expeditiously as possible, use
     its best efforts to effect the registration on Form S-3 (or such successor
     form) of all Registrable Shares which the Company has been requested to so
     register.

                (b) The Company shall not be required to effect more than two
     registrations pursuant to paragraph (a) above.

                (c) If at the time of any request to register Registrable Shares
     pursuant to this Section 1.2, the Company is engaged or has fixed plans to
     engage within 30 days of the time of the request in a registered public
     offering as to which the Stockholders may include Registrable Shares
     pursuant to Section 1.3 or is engaged in any other activity which, in the
     good faith determination of the Company's Board of Directors, would be
     adversely affected by the requested registration to the material detriment
     of the Company, then the Company may at its option direct that such request
     be delayed for a period not in excess of six months from the effective date
     of such offering or the date of commencement of such other material
     activity, as the case may be, such right to delay a request to be exercised
     by the Company not more than once in any two-year period.

                                       2
<PAGE>

        1.3  Incidental Registration.

                (a) Whenever the Company proposes to file a Registration
Statement (other than pursuant to Section 1.2) at any time and from time to
time, it will, prior to such filing, give written notice to all Stockholders of
its intention to do so and, upon the written request of a Stockholder or
Stockholders given within 20 days after the Company provides such notice (which
request shall state the intended method of disposition of such Registrable
Shares), the Company shall use its best efforts to cause all Registrable Shares
which the Company has been requested by such Stockholder or Stockholders to
register to be registered under the Securities Act to the extent necessary to
permit their sale or other disposition in accordance with the intended methods
of distribution specified in the request of such Stockholder or Stockholders;
provided that the Company shall have the right to postpone or withdraw any
registration effected pursuant to this Section 1.3 without obligation to any
Stockholder.

                (b) In connection with any registration under this Section 1.3
involving an underwriting, the Company shall not be required to include (i) any
Registrable Shares in such registration unless the holders thereof accept the
terms of the underwriting as agreed upon between the Company and the
underwriters selected by it (provided that such terms must be consistent with
this Agreement), or (ii) except in the Company's initial public offering of
Common Stock or any Registration Statement filed by the Company with the
Commission within 24 months after the closing of such initial public offering,
any Registrable Shares then eligible for resale under Rule 144(k) under the
Securities Act. If in the opinion of the managing underwriter it is appropriate
because of marketing factors to limit the number of Registrable Shares to be
included in the offering, then the Company shall be required to include in the
registration only that number of Registrable Shares, if any, which the managing
underwriter believes should be included therein. If the number of Registrable
Shares to be included in the offering in accordance with the foregoing is less
than the total number of shares which the holders of Registrable Shares have
requested to be included, then the holders of Registrable Shares who have
requested registration and other holders of securities entitled to include them
in such registration shall participate in the registration pro rata based upon
their total ownership of shares of Common Stock (giving effect to the conversion
into Common Stock of all securities convertible thereinto). For purposes of
making any such reduction, each stockholder which is a partnership, together
with the affiliates, partners and retired partners of such stockholder, the
estates and family members of any such partners and retired partners and of
their spouses, and any trusts for the benefit of any of the foregoing persons
shall be deemed to be a single "holder", and any pro-rata reduction with respect
to such "holder" shall be based upon the aggregate amount of Registrable Shares
owned by all entities and individuals included in such "holder", as defined in
this sentence (and the aggregate amount so allocated to such "holder" shall be
allocated among the entities and individuals included in such "holder" in such
manner as such stockholder may reasonably determine). If any holder would thus
be entitled to include more securities than such holder requested to be
registered, the excess shall be allocated among other requesting holders pro
rata in the manner described in this paragraph.

                                       3
<PAGE>

        1.4 Registration Procedures. If and whenever the company is required by
the provisions of this Agreement to use its best efforts to effect the
registration of any of the Registrable Shares under the Securities Act, the
Company shall:

        (a) file with the Commission a Registration Statement with respect to
     such Registrable Shares and use its best efforts to cause that Registration
     Statement to become and remain effective;

        (b) as expeditiously as possible prepare and file with the Commission
any amendments and supplements to the Registration Statement and the prospectus
included in the Registration Statement as may be necessary to keep the
Registration Statement effective, in the case of a firm commitment underwritten
public offering, until each underwriter has completed the distribution of all
securities purchased by it and, in the case of any other offering, until the
earlier of the sale of all Registrable Shares covered thereby or 120 days after
the effective date thereof;

        (c) as expeditiously as possible furnish to each selling Stockholder
such reasonable numbers of copies of the prospectus, including a preliminary
prospectus, in conformity with the requirements of the Securities Act, and such
other documents as the selling Stockholder may reasonably request in order to
facilitate the public sale or other disposition of the Registrable Shares owned
by the selling Stockholder; and

        (d) as expeditiously as possible use its best efforts to register or
qualify the Registrable Shares covered by the Registration Statement under the
securities or Blue Sky laws of such states as the selling Stockholders shall
reasonably request, and do any and all other acts and things that may be
necessary or desirable to enable the selling Stockholders to consummate the
public sale or other disposition in such states of the Registrable Shares owned
by the selling Stockholder; provided, however, that the Company shall not be
required in connection with this paragraph (d) to qualify as a foreign
corporation or execute a general consent to service of process in any
jurisdiction.

     If the Company has delivered preliminary or final prospectuses to the
selling Stockholders and after having done so the prospectus is amended to
comply with the requirements of the Securities Act, the Company shall promptly
notify the selling Stockholders and, if requested, the selling Stockholders
shall immediately cease making offers of Registrable Shares and return all
prospectuses to the Company.  The Company shall promptly provide the selling
Stockholders with revised prospectuses and, following receipt of the revised
prospectuses, the selling Stockholders shall be free to resume making offers of
the Registrable Shares.

        1.5 Allocation of Expenses. The Company will pay all Registration
Expenses of all registrations under this Agreement; provided, however, that if a
registration under Section 1.2 is withdrawn at the request of the Stockholders
requesting such registration (other than as a result of information concerning
the business or financial condition of the Company which is made known to the
Stockholders after the date on which such registration was requested) and if the
requesting Stockholders elect not to have such registration counted as a
registration requested under Section 1.2, the requesting Stockholders shall pay
the Registration Expenses of such registration pro rata in accordance with the
number of their Registrable Shares included in such registration. For purposes
of this Section 1.5, the term "Registration Expenses" shall mean all expenses
incurred by the Company in complying with this Agreement, including, without
limitation, all registration and filing fees, exchange listing fees, printing
expenses, fees and expenses of counsel for the Company and the fees

                                       4
<PAGE>

and expenses of one counsel selected by the selling Stockholders to represent
the selling Stockholders, state Blue Sky fees and expenses, and the expense of
any special audits incident to or required by any such registration, but
excluding underwriting discounts, selling commissions and the fees and expenses
of selling Stockholders' own counsel (other than the counsel selected to
represent all selling Stockholders).

     1.6  Indemnification and Contribution.

        (a) In the event of any registration of any of the Registrable Shares
under the Securities Act pursuant to this Agreement, the Company will indemnify
and hold harmless the seller of such Registrable Shares, each underwriter of
such Registrable Shares, and each other person, if any, who controls such seller
or underwriter within the meaning of the Securities Act or the Exchange Act
against any losses, claims, damages or liabilities, joint or several, to which
such seller, underwriter or controlling person may become subject under the
Securities Act, the Exchange Act, state securities or Blue Sky laws 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 Registrable Shares were registered under the Securities Act,
any preliminary prospectus or final prospectus contained in the Registration
Statement, or any amendment or supplement to such Registration Statement, or
arise out of or are based upon the omission or alleged omission to state a
material fact required to be stated therein or necessary to make the statements
therein not misleading; and the Company will reimburse such seller, underwriter
and each such controlling person for any legal or any other expenses reasonably
incurred by such seller, underwriter or controlling person 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 to the
extent that any such loss, claim, damage or liability arises out of or is based
upon any untrue statement or omission made in such Registration Statement,
preliminary prospectus or final prospectus, or any such amendment or supplement,
in reliance upon and in conformity with information furnished to the Company, in
writing, by or on behalf of such seller, underwriter or controlling person
specifically for use in the preparation thereof.

        (b) In the event of any registration of any of the Registrable Shares
under the Securities Act pursuant to this Agreement, each seller of Registrable
Shares, severally and not jointly, will indemnify and hold harmless the Company,
each of its directors and officers and each underwriter (if any) and each
person, if any, who controls the Company or any such underwriter within the
meaning of the Securities Act or the Exchange Act, against any losses, claims,
damages or liabilities, joint or several, to which the Company, such directors
and officers, underwriter or controlling person may become subject under the
Securities Act, Exchange Act, state securities or Blue Sky laws 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 a material fact contained in any Registration Statement under which
such Registrable Shares were registered under the Securities Act, any
preliminary prospectus or final prospectus contained in the Registration
Statement, or any amendment or supplement to the Registration Statement, or
arise out of or are based upon any omission or alleged omission to state a
material fact required to be stated therein or necessary to make the statements
therein not misleading, if the statement or omission was made in reliance upon
and in

                                       5
<PAGE>

conformity with information relating to such seller furnished in writing to the
Company by or on behalf of such seller specifically for use in connection with
the preparation of such Registration Statement, prospectus, amendment or
supplement; provided, however, that the obligations of each Stockholder
hereunder shall be limited to an amount equal to the net proceeds received by
such Stockholder from Registrable Shares sold in connection with such
registration.

        (c) Each party entitled to indemnification under this Section 1.6 (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, provided, further, that the failure of any Indemnified Party to
give notice as provided herein shall not relieve the Indemnifying Party of its
obligations under this Section 1.6. The Indemnified Party may participate in
such defense at such party's expense; provided, however, that the Indemnifying
Party shall pay such expense 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 the 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 of such claim or litigation, and no Indemnified Party shall
consent to entry of any judgment or settle such claim or litigation without the
prior written consent of the Indemnifying Party.

        (d) In order to provide for just and equitable contribution to joint
liability under the Securities Act in any case in which either (i) any holder of
Registrable Shares exercising rights under this Agreement, or any controlling
person of any such holder, makes a claim for indemnification pursuant to this
Section 1.6 but it is judicially determined (by the entry of a final judgment or
decree by a court of competent jurisdiction and the expiration of time to appeal
or the denial of the last right of appeal) that such indemnification may not be
enforced in such case notwithstanding the fact that this Section 1.6 provides
for indemnification in such case, or (ii) contribution under the Securities Act
may be required on the part of any such selling Stockholder or any such
controlling person in circumstances for which indemnification is provided under
this Section 1.6; then, in each such case, the Company and such Stockholder will
contribute to the aggregate losses, claims, damages or liabilities to which they
may be subject (after contribution from others) in such proportions so that such
holder is responsible for the portion represented by the percentage that the
public offering price of its Registrable Shares offered by the Registration
Statement bears to the public offering price of all securities offered by such
Registration Statement, and the Company is responsible for the remaining
portion; provided, however, that, in any such case, (A) no such holder will be
required to contribute any amount in excess of the net proceeds to it of all
Registrable Shares sold by it pursuant to such Registration Statement, and (B)
no person or entity guilty of fraudulent misrepresentation, within the meaning
of Section 11(f) of the Securities Act, shall be entitled to contribution from
any person or entity who is not guilty of such fraudulent misrepresentation.

                                       6
<PAGE>

        1.7 Indemnification with Respect to Underwritten Offering. In the event
that Registrable Shares are sold pursuant to a Registration Statement in an
underwritten offering pursuant to Section 1.2, the Company agrees to enter into
an underwriting agreement containing customary representations and warranties
with respect to the business and operations of an issuer of the securities being
registered and customary covenants and agreements to be performed by such
issuer, including without limitation customary provisions with respect to
indemnification by the Company of the underwriters of such offering.

        1.8 Information by Holder. Each Stockholder including Registrable Shares
in any registration shall furnish to the Company such information regarding such
Stockholder and the distribution proposed by such Stockholder as the Company may
reasonably request in writing and as shall be required in connection with any
registration, qualification or compliance referred to in this Agreement.

        1.9 "Stand-Off" Agreement. Each Stockholder, if requested by the Company
and the managing underwriter of an offering by the Company of Common Stock or
other securities of the Company pursuant to a Registration Statement, shall
agree not to sell publicly or otherwise transfer or dispose of any Registrable
Shares or other securities of the Company held by such Stockholder for a period
of 180 days following the effective date of such Registration Statement;
provided, that:

             (a) such agreement shall only apply to the Registration Statement
covering the Company's initial public offering of Common Stock in an
underwritten offering; and

             (b) all officers and directors of the Company shall enter into
similar agreements.

        1.10 Rule 144 Requirements. After the earliest of (i) the closing of the
sale of securities of the Company pursuant to a Registration Statement, (ii) the
registration by the Company of a class of securities under Section 12 of the
Exchange Act, or (iii) the issuance by the Company of an offering circular
pursuant to Regulation A under the Securities Act, the Company agrees to:

             (a) comply with the requirements of Rule 144(c) under the
Securities Act with respect to current public information about the Company;

             (b) use its best efforts to file with the Commission 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

             (c) furnish to any holder of Registrable Shares upon request (i) a
written statement by the Company as to its compliance with the requirements of
said Rule 144(c), and the reporting requirements 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 of the Company as such
holder may reasonably request to avail itself of any similar rule or regulation
of the Commission allowing it to sell any such securities without registration.

                                       7
<PAGE>

        1.11 Termination. All of the Company's obligations to register
Registrable Shares under this Agreement shall terminate on the date seven years
after the closing of the Company's initial public offering of Common Stock
pursuant to a Registration Statement.

        2. Transfers of Rights. This Agreement, and the rights and obligations
of each Purchaser hereunder, may be assigned by such Purchaser to any person or
entity to which at least 100,000 Shares are transferred by such Purchaser, and
such transferee shall be deemed a "Purchase" for purposes of this Agreement;
provided that the transferee provides written notice of such assignment to the
Company and agrees to be bound hereby and provided further that the transferee
is not a competitor of the Company.

        3.  General.

                (a) Notices. All notices, requests, consents, and other
communications under this Agreement shall be in writing and shall be delivered
by hand or mailed by first class certified or registered mail, return receipt
requested, postage prepaid:

     If to the Company, at 45 Moulton Street, Cambridge, Massachusetts 02138,
Attention: President, or at such other address or addresses as may have been
furnished in writing by the Company to the Purchaser, with a copy to Mark G.
Borden, Esq., Hale and Dorr, 60 State Street, Boston, Massachusetts 02109; or

     If to a Purchaser, at his or its address set forth in the Series C Purchase
Agreement, or at such other address or addresses as may have been furnished to
the Company in writing by such Purchaser.

                (b) Entire Agreement. This Agreement embodies the entire
agreement and understanding between the parties hereto with respect to the
subject matter hereof and supersedes all prior agreements and understandings
relating to such subject matter.

                (c) Amendments and Waivers. Any term of this Agreement may be
amended and the observance of any term of this Agreement may be waived (either
generally or in a particular instance and either retroactively or
prospectively), with the written consent of the Company and the holders of at
least 66 2/3% of the then outstanding Registrable Shares (including shares
issued upon conversion thereof). No waivers of or exceptions to any term,
condition or provision of this Agreement, in any one or more instances, shall be
deemed to be, or construed as, a further or continuing waiver of any such term,
condition or provision.

                (d) Counterparts. This Agreement may be executed in one or more
counterparts, each of which shall be deemed to be an original, but all of which
shall be one and the same document.

                (e) Severability. The invalidity or unenforceability of any
provision of this Agreement shall not affect the validity or enforceability of
any other provision of this Agreement.

                (f) Governing Law. This Agreement shall be governed by and
construed in accordance with the laws of the Commonwealth of Massachusetts.

                                       8
<PAGE>

     IN WITNESS WHEREOF, the parties hereto have set their hands as of the date
first written above:

                              COMPANY:

                              ONTOGENY, INC.

                              /s/ William W. Helman
                              ---------------------
                              William W. Helman, President

                              Dated:

                              PURCHASER:

                              BIOGEN, INC.

                              By:/s/ James R. Tobin
                                 ------------------

                              Dated:

                                       9