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                                                                    Exhibit 10.2

                           IDERA PHARMACEUTICALS, INC.

                          REGISTRATION RIGHTS AGREEMENT

     REGISTRATION RIGHTS AGREEMENT (this "AGREEMENT"), dated as of March 24,
2006, by and among IDERA PHARMACEUTICALS, INC., a corporation organized under
the laws of the State of Delaware (the "COMPANY"), and the undersigned the
"PURCHASERS".

                                    WHEREAS:

     In connection with the Common Stock Purchase Agreement, dated as of March
24, 2006, by and among the Company and the Purchasers (the "STOCK PURCHASE
AGREEMENT"), the Company has agreed, upon the terms and subject to the
conditions contained therein, to issue and sell to the Purchasers (i) shares
(the "SHARES") of the Company's common stock, par value $0.001 per share (the
"COMMON STOCK"), and (ii) warrants (the "WARRANTS") to acquire shares of Common
Stock. The shares of Common Stock issuable upon exercise of or otherwise
pursuant to the Warrants are referred to herein as the "WARRANT SHARES."

     To induce the Purchasers to execute and deliver the Stock Purchase
Agreement, the Company has agreed to provide certain registration rights under
the Securities Act of 1933, as amended, and the rules and regulations
thereunder, or any similar successor statute (collectively, the "SECURITIES
ACT"), and applicable state securities laws.

     NOW, THEREFORE, in consideration of the premises and the mutual covenants
contained herein and other good and valuable consideration, the receipt and
sufficiency of which are hereby acknowledged, the Company and the Purchasers
hereby agree as follows:

     1. DEFINITIONS.

          (A) As used in this Agreement, the following terms shall have the
following meanings:

               (I) "PURCHASERS" means the Purchasers and any transferees or
assignees who agree to become bound by the provisions of this Agreement in
accordance with Section 10 hereof.

               (II) "REGISTER," "REGISTERED," and "REGISTRATION" refer to a
registration effected by preparing and filing a Registration Statement or
Statements in compliance with the Securities Act and pursuant to Rule 415 under
the Securities Act or any successor rule providing for offering securities on a
continuous basis ("RULE 415"), and the declaration or ordering of effectiveness
of such Registration Statement by the United States Securities and Exchange
Commission (the "SEC").

               (III) "REGISTRABLE SECURITIES" means (a) the Shares, (b) the
Warrant Shares and (c) any shares of capital stock issued or issuable, from time
to time (with any adjustments), in respect of the Shares or the Warrant Shares
by virtue of any stock split, stock dividend, recapitalization or similar event;
provided, however, that shares of Common Stock that are Registrable Securities
shall cease to be Registrable Securities upon the earliest of (A) the date


                                       1.

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that such shares are eligible to be sold under Rule 144(k) of the Securities
Act, (B) the date that such shares are sold (I) pursuant to a registration
statement, (II) to or through a broker, dealer or underwriter in a public
securities transaction and/or (III) in a transaction exempt from the
registration and prospectus delivery requirements of the Securities Act such
that all transfer restrictions and restrictive legends with respect thereto, if
any, are removed upon the consummation of such sale, or (C) any sale or transfer
to any Person which by virtue of Section 10 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 Securities, the determination of such percentage shall include
shares of Common Stock issuable upon exercise of the Warrants to the extent any
such Warrants are outstanding, even if such exercise has not been effected.

               (IV) "REGISTRATION STATEMENT" means a registration statement of
the Company under the Securities Act.

          (B) Capitalized terms used herein and not otherwise defined herein
shall have the respective meanings set forth in the Securities Purchase
Agreement.

     2. REGISTRATION.

          (A) MANDATORY REGISTRATION. The Company shall prepare promptly and
file with the SEC as soon as practicable, but in no event later than the
thirtieth (30th) day following the date hereof (the "FILING DATE"), a
Registration Statement on Form S-3 (or, if Form S-3 is not then available, on
such form of Registration Statement as is then available to effect a
registration of all of the Registrable Securities, covering the resale of the
Registrable Securities. The Registration Statement filed hereunder, to the
extent allowable under the Securities Act and the Rules promulgated thereunder
(including Rule 416), shall state that such Registration Statement also covers
such indeterminate number of additional shares of Common Stock as may become
issuable upon exercise of the Warrants to prevent dilution resulting from stock
splits, stock dividends or similar transactions.

          (B) PAYMENTS BY THE COMPANY. The Company shall use its best efforts to
cause the Registration Statement required to be filed pursuant to Section 2(a)
hereof to become effective as soon as practicable after the Filing Date. At the
time of effectiveness, the Company shall ensure that such Registration Statement
covers all of the Registrable Securities (including, if necessary, by filing an
amendment prior to the effective date of the Registration Statement to increase
the number of shares covered thereby). If (i) the Registration Statement
required to be filed by the Company pursuant to Section 2(a) hereof is not filed
with the SEC prior to the Filing Date or declared effective by the SEC on or
before the one hundred twentieth (120th) day after the date hereof (the
"REGISTRATION DEADLINE") or, (ii) if, after any such Registration Statement has
been declared effective by the SEC, sales of any of the Registrable Securities
required to be covered by such Registration Statement cannot be made pursuant to
such Registration Statement because such Registration Statement has been
suspended (by reason of a stop order or the Company's failure to update the
Registration Statement or otherwise) except as a result of a permitted
Suspension under Section 9, then the Company will make payments to the
Purchasers in such amounts and at such times as shall be determined pursuant to
this Section 2(b) as liquidated damages and not as a penalty for such delay in
or reduction of their ability to sell the


                                       2.

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Registrable Securities (which remedy shall constitute the Purchasers exclusive
monetary remedy). The Company shall pay to each Purchaser an amount equal to the
product of (i) the aggregate purchase price of the Shares and Warrant Shares
then held by such Purchaser (the "AGGREGATE SHARE PRICE"), multiplied by (ii)
one hundredths (.01), for each thirty (30) day period (or portion thereof) (A)
after the Filing Date and prior to the date the Registration Statement is filed
with the SEC pursuant to Section 2(a), (B) after the Registration Deadline and
prior to the date the Registration Statement filed pursuant to Section 2(a) is
declared effective by the SEC, and (C) during which sales of any Registrable
Securities cannot be made pursuant to any such Registration Statement after the
Registration Statement has been declared effective; provided, however, that
there shall be excluded from each such period any delays which are solely
attributable to changes (other than corrections of Company mistakes with respect
to information previously provided by the Purchasers) required by the Purchasers
in the Registration Statement with respect to information relating to the
Purchasers, including, without limitation, changes to the plan of distribution.
Such amounts shall be paid in cash within five (5) days after the end of each
period that gives rise to such obligation, provided that, if any such period
extends for more than thirty (30) days, interim payments shall be made for each
such thirty (30) day period. Notwithstanding the foregoing, in no event shall
the Company be obligated to pay liquidated damages (a) to more than one
Purchaser in respect of the same Securities for the same period of time or (b)
in an aggregate amount that exceeds 10% of the purchase price paid by such
Purchaser for such Shares and Warrant Shares.

     3. OBLIGATIONS OF THE COMPANY.

     In connection with the registration of the Registrable Securities, the
Company shall have the following obligations:

          (A) The Company shall respond promptly to any and all comments made by
the staff of the SEC to the Registration Statement required by Section 2(a), and
shall submit to the SEC before the close of business on a business day within
five business days after the business day on which the Company learns (either by
telephone or in writing) that no review of such Registration Statement will be
made by the SEC or that the staff of the SEC has no further comments on such
Registration Statement, as the case may be, a request for acceleration of the
effectiveness of such Registration Statement to a time and date as soon as
practicable. The Company shall use its best efforts to keep such Registration
Statement effective pursuant to Rule 415 at all times until no Registrable
Securities remain outstanding (the "REGISTRATION PERIOD"). The Registration
Statement (including any amendments or supplements thereto and prospectuses
contained therein and all documents incorporated by reference therein) (i) shall
comply in all material respects with the requirements of the Securities Act and
the rules and regulations of the SEC promulgated thereunder and (ii) shall not
contain any untrue statement of a material fact or omit to state a material fact
required to be stated therein, or necessary to make the statements therein not
misleading.

          (B) The Company shall prepare and file with the SEC such amendments
(including post-effective amendments) and supplements to the Registration
Statement and the prospectus used in connection with the Registration Statement
as may be necessary to keep the Registration Statement effective at all times
during the Registration Period, and, during such period, comply with the
provisions of the Securities Act with respect to the disposition of all


                                       3.

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Registrable Securities of the Company covered by the Registration Statement
until such time as all of such Registrable Securities have been disposed of in
accordance with the intended methods of disposition by the seller or sellers
thereof as set forth in the Registration Statement.

          (C) The Company shall furnish to each Purchaser whose Registrable
Securities are included in the Registration Statement (i) promptly after the
same is prepared and publicly distributed or filed with the SEC, one copy of the
Registration Statement and any amendment thereto, each preliminary prospectus
and prospectus and each amendment or supplement thereto, (ii) to the extent not
publicly available on the SEC's EDGAR system, promptly after the same is filed
with the SEC or received by the Company, one copy of each letter written by or
on behalf of the Company to the SEC or the staff of the SEC (including, without
limitation, any request to accelerate the effectiveness of the Registration
Statement or amendment thereto) and each item of correspondence from the SEC or
the staff of the SEC, in each case relating to the Registration Statement (other
than any portion, if any, thereof which contains information for which the
Company has sought or intends to seek confidential treatment); (iii) within 24
hours of the date of effectiveness of the Registration Statement or any
amendment thereto, a notice stating that the Registration Statement or amendment
has been declared effective; and (iv) such number of copies of a prospectus,
including a preliminary prospectus, and all amendments and supplements thereto
and such other documents as such Purchaser may reasonably request in order to
facilitate the disposition of the Registrable Securities owned by such
Purchaser. Notwithstanding the foregoing, the Company shall not send to any
Purchaser any document pursuant to clause (ii) above that the Company determines
contains material nonpublic information unless prior to transmittal of such
document the Company and such Purchaser agree otherwise and such Purchaser
enters into an appropriate confidentiality agreement with the Company with
respect thereto.

          (D) The Company shall use its best efforts to (i) register and qualify
the Registrable Securities covered by the Registration Statement under such
other securities or "blue sky" laws of such jurisdictions in the United States
as each Purchaser who holds Registrable Securities being offered reasonably
requests, (ii) prepare and file in those jurisdictions such amendments
(including post-effective amendments) and supplements to such registrations and
qualifications as may be necessary to maintain the effectiveness thereof during
the Registration Period, (iii) take such other actions as may be necessary to
maintain such registrations and qualifications in effect at all times during the
Registration Period, and (iv) take all other actions reasonably necessary or
advisable to qualify the Registrable Securities for sale in such jurisdictions;
provided, however, that the Company shall not be required in connection
therewith or as a condition thereto to (a) qualify to do business in any
jurisdiction where it would not otherwise be required to qualify but for this
Section 3(d), (b) subject itself to general taxation in any such jurisdiction,
(c) file a general consent to service of process in any such jurisdiction, (d)
provide any undertakings that cause the Company undue expense or burden, or (e)
make any change in its charter or by-laws, which in each case the Board of
Directors of the Company determines to be contrary to the best interests of the
Company and its stockholders.

          (E) As promptly as practicable after becoming aware of such event, the
Company shall notify each Purchaser by telephone and facsimile of the happening
of any event, of which the Company has knowledge, as a result of which the
prospectus included in the Registration Statement, as then in effect, includes
an untrue statement of a material fact or


                                       4.

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omission to state a material fact required to be stated therein or necessary to
make the statements therein not misleading, shall use its best efforts promptly
to prepare a supplement or amendment to the Registration Statement to correct
such untrue statement or omission, and, following such filing and, if
applicable, the effectiveness of such filing, shall deliver such number of
copies of such supplement or amendment to each Purchaser as such Purchaser may
reasonably request. In no event shall the Company disclose to any Purchaser any
material-non-public information, including without limitation the event, the
untrue statement or the omission.

          (F) The Company shall use its best efforts (i) to prevent the issuance
of any stop order or other suspension of effectiveness of a Registration
Statement, and, if such an order is issued, to obtain the withdrawal of such
order at the earliest practicable moment (including in each case by amending or
supplementing such Registration Statement) and (ii) to notify each Purchaser who
holds Registrable Securities being sold (or, in the event of an underwritten
offering, the managing underwriters) of the issuance of such order and the
resolution thereof (and if such Registration Statement is supplemented or
amended, deliver such number of copies of such supplement or amendment to each
Purchaser as such Purchaser may reasonably request).

          (G) The Company shall permit a single firm of counsel designated by
the Purchasers to review the Registration Statement and all amendments and
supplements thereto a reasonable period of time prior to its filing with the SEC
and shall consider in good faith and consult with such counsel regarding any
comment such counsel may reasonably make.

          (H) The Company shall make generally available to its security holders
as soon as practical, but not later than ninety (90) days after the first
anniversary of the close of the fiscal quarter during which the Registration
Statement was declared effective, an earnings statement (in form complying with
the provisions of Rule 158 under the Securities Act) covering a twelve-month
period beginning not later than the first day of the Company's fiscal quarter
next following the effective date of the Registration Statement.

          (I) At the request of any Purchaser in the case of an underwritten
public offering, the Company shall furnish, on the date of effectiveness of the
Registration Statement (i) an opinion, dated as of such date, from counsel
representing the Company addressed to the underwriters and in form, scope and
substance as is customarily given in an underwritten public offering and (ii) a
letter, dated such date, from the Company's independent certified public
accountants in form and substance as is customarily given by independent
certified public accountants to underwriters in an underwritten public offering,
addressed to the underwriters, if any.

          (J) For the sole purpose of enabling the Purchasers to conduct an
investigation as to the accuracy of the Registration Statement for the purpose
of reducing or eliminating the Purchasers' liability under the Securities Act,
the Company shall make available for inspection by one firm of attorneys and one
firm of accountants or other agents retained by the Purchasers (collectively,
the "INSPECTORS") following reasonable notice all pertinent financial and other
records, and pertinent corporate documents and properties of the Company
(collectively, the "RECORDS"), as shall be reasonably deemed necessary by each
Inspector to enable each Inspector to exercise its due diligence responsibility,
and cause the Company's officers to supply such information which any Inspector
may reasonably request for purposes of


                                       5.

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such due diligence. Nothing herein shall be deemed to limit the Purchasers'
ability to sell Registrable Securities in a manner which is otherwise consistent
with applicable laws and regulations. The Company shall not disclose material
nonpublic information to the Inspectors unless the Company and the Purchasers
agree and the Purchasers and the Inspectors enter into an appropriate
confidentiality agreement with the Company with respect thereto.

          (K) The Company shall provide a transfer agent and registrar, which
may be a single entity, for the Registrable Securities not later than the
effective date of the Registration Statement.

          (L) The Company shall cooperate with the Purchasers who hold
Registrable Securities being to facilitate the timely preparation and delivery
of certificates representing Registrable Securities to be offered pursuant to
the Registration Statement and enable such certificates to be in such
denominations or amounts, as the case may be, as Purchasers may reasonably
request and registered in such names as the Purchasers may request.

          (M) At the reasonable request of the Purchasers holding a majority in
interest of the Registrable Securities, the Company shall prepare and file with
the SEC such amendments (including post-effective amendments) and supplements to
a Registration Statement and the prospectus used in connection with such
Registration Statement as may be necessary in order to change the plan of
distribution set forth in such Registration Statement.

          (N) From and after the date of this Agreement, the Company shall not,
and shall not agree to, allow the holders of any securities of the Company to
include any of their securities which are not Registrable Securities in the
Registration Statement under Section 2(a) hereof or any amendment or supplement
thereto under Section 3(b) hereof without the consent of the holders of a
majority in interest of the Registrable Securities.

          (O) Prior to the effectiveness of the Registration Statement, the
Company shall take all actions necessary to meet the "registrant eligibility"
requirements set forth in the general instructions to Form S-3 or any successor
form thereto, to continue to be eligible to register the resale of its Common
Stock on a registration statement on Form S-3 under the Securities Act.

     4. OBLIGATIONS OF THE PURCHASERS. In connection with the registration of
the Registrable Securities, the Purchasers shall have the following obligations:

          (A) It shall be a condition precedent to the obligations of the
Company under Sections 2 and 3 with respect to the Registrable Securities of a
particular Purchaser that such Purchaser shall furnish to the Company such
information regarding itself, the Registrable Securities held by it and the
intended method of disposition of the Registrable Securities held by it as shall
be reasonably required to effect the registration of such Registrable Securities
and shall execute such documents in connection with such registration as the
Company may reasonably request. At least five trading days prior to the first
anticipated filing date of the Registration Statement, the Company shall notify
each Purchaser of the information the Company requires from each such Purchaser.

          (B) Each Purchaser, by such Purchaser's acceptance of the Registrable
Securities, agrees to cooperate with the Company as reasonably requested by the
Company in


                                       6.

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connection with the preparation and filing of the Registration Statement
hereunder, unless such Purchaser has notified the Company in writing of such
Purchaser's election to exclude all of such Purchaser's Registrable Securities
from such Registration Statement.

          (C) Each Purchaser agrees that, upon receipt of any notice from the
Company of the happening of any event of the kind described in Sections 3(e),
3(f) or 9, such Purchaser will immediately discontinue disposition of
Registrable Securities pursuant to the Registration Statement covering such
Registrable Securities until such Purchaser's receipt of the copies of the
supplemented or amended prospectus contemplated by Sections 3(e), 3(f) or 9.

     5. EXPENSES OF REGISTRATION. All reasonable expenses incurred by the
Company or the Purchasers in connection with registrations, filings or
qualifications pursuant to Sections 2 and 3 above, including, without
limitation, all registration, listing and qualifications fees, printers and
accounting fees, the fees and disbursements of counsel for the Company, the fees
and disbursements of one counsel selected by the Purchasers, and the
underwriting discounts and commissions shall be borne by the Company. In the
event that one party breaches this Agreement, such party shall pay all of the
other party's costs and expenses (including reasonable legal fees) incurred by
such other party in connection with the enforcement of such other party's rights
hereunder.

     6. INDEMNIFICATION. In the event any Registrable Securities are included in
a Registration Statement under this Agreement:

          (A) To the extent permitted by law, the Company will indemnify, hold
harmless and defend (i) each Purchaser who holds such Registrable Securities,
and (ii) the directors, officers, partners, members, employees and agents of
such Purchaser and each person who controls any Purchaser within the meaning of
Section 15 of the Securities Act or Section 20 of the Securities Exchange Act of
1934, as amended (the "EXCHANGE ACT"), if any, (each, an "INDEMNIFIED PERSON"),
against any joint or several losses, claims, damages, liabilities or expenses
(collectively, together with actions, proceedings or inquiries by any regulatory
or self-regulatory organization, whether commenced or threatened, in respect
thereof, "CLAIMS") to which any of them may become subject insofar as such
Claims arise out of or are based upon: (i) any untrue statement or alleged
untrue statement of a material fact in a Registration Statement or the omission
or alleged omission to state therein a material fact required to be stated or
necessary to make the statements therein not misleading, (ii) any untrue
statement or alleged untrue statement of a material fact contained in any
preliminary prospectus if used prior to the effective date of such Registration
Statement, or contained in the final prospectus (as amended or supplemented, if
the Company files any amendment thereof or supplement thereto with the SEC) or
the omission or alleged omission to state therein any material fact necessary to
make the statements made therein, in light of the circumstances under which the
statements therein were made, not misleading, or (iii) any violation or alleged
violation by the Company of the Securities Act, the Exchange Act, any other law,
including, without limitation, any state securities law, or any rule or
regulation thereunder relating to the offer or sale of the Registrable
Securities (the matters in the foregoing clauses (i) through (iii),
collectively, "VIOLATIONS"). Subject to the restrictions set forth in Section
6(c) with respect to the number of legal counsel, the Company shall reimburse
the Purchasers and each other Indemnified Person, promptly as such expenses are
incurred and are due and payable, for any reasonable legal fees or other
reasonable expenses


                                       7.

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incurred by them in connection with investigating or defending any such Claim.
Notwithstanding anything to the contrary contained herein, the indemnification
agreement contained in this Section 6(a): (i) shall not apply to a Claim arising
out of or based upon (A) a Violation which occurs in reliance upon and in
conformity with information furnished in writing to the Company by such
Indemnified Person expressly for use in the Registration Statement or any such
amendment thereof or supplement thereto, (B) the failure of a Purchaser to
comply with Section 4(c) or (C) the use by a Purchaser in connection with any
sale or sales of Registrable Securities of a prospectus containing any untrue
statement or omission of a material fact following notification by the Company
that such prospectus contains an untrue statement or omission of a material fact
and receipt by the Purchaser of a corrected prospectus; and (ii) shall not apply
to amounts paid in settlement of any Claim if such settlement is effected
without the prior written consent of the Company, which consent shall not be
unreasonably withheld. Such indemnity shall remain in full force and effect
regardless of any investigation made by or on behalf of the Indemnified Person
and shall survive the transfer of the Registrable Securities by the Purchasers
pursuant to Section 10 hereof.

          (B) Each Purchaser who holds such Registrable Securities agrees
severally and not jointly to indemnify, hold harmless and defend, to the same
extent and in the same manner set forth in Section 6(a), the Company, each of
its directors, each of its officers who signs the Registration Statement, its
employees, agents and each person, if any, who controls the Company within the
meaning of Section 15 of the Securities Act or Section 20 of the Exchange Act,
and any other stockholder selling securities pursuant to the Registration
Statement or any of its directors or officers or any person who controls such
stockholder within the meaning of the Securities Act or the Exchange Act
(collectively and together with an Indemnified Person, an "INDEMNIFIED PARTY"),
against any Claim to which any of them may become subject, under the Securities
Act, the Exchange Act or otherwise, insofar as such Claim arises out of or is
based upon any Violation, in each case to the extent (and only to the extent)
that such Violation occurs in reliance upon and in conformity with written
information furnished to the Company by such Purchaser expressly for use in
connection with such Registration Statement; and subject to Section 6(c) such
Purchaser will reimburse any legal or other expenses (promptly as such expenses
are incurred and are due and payable) reasonably incurred by them in connection
with investigating or defending any such Claim; provided, however, that (I) the
indemnity agreement contained in this Section 6(b) shall not apply to amounts
paid in settlement of any Claim if such settlement is effected without the prior
written consent of such Purchaser, which consent shall not be unreasonably
withheld, and (II) the Purchaser shall be liable under this Agreement (including
this Section 6(b) and Section 7) for only that amount as does not exceed the net
proceeds actually received by such Purchaser as a result of the sale of
Registrable Securities pursuant to such Registration Statement. Such indemnity
shall remain in full force and effect regardless of any investigation made by or
on behalf of such Indemnified Party and shall survive the transfer of the
Registrable Securities by the Purchasers pursuant to Section 10 hereof.

          (C) Promptly after receipt by an Indemnified Person or Indemnified
Party under this Section 6 of notice of the threat or commencement of any action
(including any governmental action), such Indemnified Person or Indemnified
Party shall, if a Claim in respect thereof is to made against any indemnifying
party under this Section 6, deliver to the indemnifying party a written notice
of the commencement thereof, and the indemnifying party shall have the right to
participate in, and, to the extent the indemnifying party so desires, jointly


                                       8.

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with any other indemnifying party similarly noticed, to assume control of the
defense thereof with counsel mutually satisfactory to the indemnifying party and
the Indemnified Person or the Indemnified Party, as the case may be; provided,
however, that such indemnifying party shall not be entitled to assume such
defense and an Indemnified Person or Indemnified Party shall have the right to
retain its own counsel with the fees and expenses to be paid by the indemnifying
party, if, in the reasonable opinion of counsel retained by the indemnifying
party, the representation by such counsel of the Indemnified Person or
Indemnified Party and the indemnifying party would be inappropriate due to
actual or potential conflicts of interest between such Indemnified Person or
Indemnified Party and any other party represented by such counsel in such
proceeding or the actual or potential defendants in, or targets of, any such
action include both the Indemnified Person or the Indemnified Party and the
indemnifying party and any such Indemnified Person or Indemnified Party
reasonably determines, based upon the reasonable opinion of counsel, that there
may be legal defenses available to such Indemnified Person or Indemnified Party
which are in conflict with those available to such indemnifying party. The
indemnifying party shall pay for only one separate legal counsel for the
Indemnified Persons or the Indemnified Parties, as applicable, and such legal
counsel shall be selected by Purchasers holding a majority-in-interest of the
Registrable Securities included in the Registration Statement to which the Claim
relates (with the approval of the Purchasers if it holds Registrable Securities
included in such Registration Statement), if the Purchasers are entitled to
indemnification hereunder, or by the Company, if the Company is entitled to
indemnification hereunder, as applicable. The failure to deliver written notice
to the indemnifying party within a reasonable time of the commencement of any
such action shall not relieve such indemnifying party of any liability to the
Indemnified Person or Indemnified Party under this Section 6, except to the
extent that the indemnifying party is actually prejudiced in its ability to
defend such action.

          (D) The Indemnified Party shall cooperate fully with the indemnifying
party in connection with any negotiation or defense of any such action or claim
by the indemnifying party and shall furnish to the indemnifying party all
information reasonably available to the Indemnified Party which relates to such
action or claim.

          (E) No indemnifying party shall, except with the consent of each
Indemnified Party (which consent shall not be unreasonably withheld), consent to
entry of any judgment or enter into any settlement which does not include the
giving by the claimant to such Indemnified Party a release from all liability in
respect to such claim or litigation.

     7. CONTRIBUTION. To the extent any indemnification by an indemnifying party
required by the terms of this Agreement is prohibited or limited by law, the
indemnifying party, in lieu of indemnifying the Indemnified Party, agrees to
contribute with respect to any amounts for which it would otherwise be liable
under Section 6 up to the amount paid or payable by the indemnifying party as a
result of the Claims in such proportion as is appropriate to reflect the
relative fault of the indemnifying party, on the one hand, and the Indemnified
Person or Indemnified Party, as the case may be, on the other hand, with respect
to the Violation giving rise to the applicable Claim; provided, however, that
(i) no contribution shall be made under circumstances where the maker would not
have been liable for indemnification under the fault standards set forth in
Section 6, (ii) no person guilty of fraudulent misrepresentation (within the
meaning of Section 11(f) of the Securities Act) shall be entitled to
contribution from any seller of Registrable Securities who was not guilty of
such fraudulent misrepresentation, and (iii)


                                       9.

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contribution (together with any indemnification or other obligations under this
Agreement) by any seller of Registrable Securities shall be limited in amount to
the net amount of proceeds received by such seller from the sale of such
Registrable Securities. The relative fault of the Company and the Purchasers
shall be determined by reference to, among other things, whether the untrue or
alleged untrue statement of material fact related to information supplied by the
Company or the Purchasers and the parties' relative intent, knowledge, access to
information and opportunity to correct or prevent such statement or omission.

     8. REPORTS UNDER THE EXCHANGE ACT. With a view to making available to the
Purchasers the benefits of Rule 144 promulgated under the Securities Act or any
other similar rule or regulation of the SEC that may at any time permit each
Purchaser to sell securities of the Company to the public, so long as the
Registration Statement is effective and such Purchaser holds Registrable
Securities, without registration ("RULE 144"), the Company agrees to:

               (I) file with the SEC in a timely manner and make and keep
available all reports and other documents required of the Company under the
Securities Act and the Exchange Act so long as the Company remains subject to
such requirements (it being understood that nothing herein shall limit the
Company's obligations under Section 5.2 of the Common Stock Purchase Agreement)
and the filing and availability of such reports and other documents is required
for the applicable provisions of Rule 144; and

               (II) furnish to each Purchaser so long as such Purchaser owns
shares of Warrants or Registrable Securities, promptly upon request, (i) a
written statement by the Company that it has complied with the reporting
requirements of Rule 144, the Securities Act and the Exchange Act, (ii) a copy
of the most recent annual or quarterly report of the Company and such other
reports and documents so filed by the Company, and (iii) such other information
as may be reasonably requested to permit the Purchasers to sell such securities
under Rule 144 without registration.

     9. SUSPENSION OF USE OF PROSPECTUS. Subject to Section 2(b), the Company
may, by written notice to the Purchasers, for a period not to exceed thirty (30)
days thereafter, (i) delay the filing of, or effectiveness of, the Registration
Statement; or (ii) suspend the Registration Statement after effectiveness and
require that the Purchasers immediately cease sales of Registrable Securities
pursuant to the Registration Statement, if (a) the Company reasonably believes
that there is or may be in existence material nonpublic information or events
involving the Company, the failure of which to be disclosed in the prospectus
included in the registration statement would result in a Violation (as defined
below) and (b) the Company shall furnish to the Purchasers a certificate signed
by the Chairman of the Board of Directors of the Company stating that in the
good faith judgment of the Board of Directors of the Company, it would have a
material adverse effect on the Company (which for this purpose shall include a
material adverse effect on a pending transaction) to disclose such material
nonpublic information or events in the prospectus included in the registration
statement (a "SUSPENSION"). The Company shall not disclose such information or
events to any Purchaser. If the Company requires the Purchasers to cease sales
of Registrable Securities pursuant to a Suspension, the Company shall, as
promptly as practicable following the termination of the circumstance which
entitled the Company to do so, take such actions as may be necessary to
reinstate the


                                      10.

<PAGE>

effectiveness of the Registration Statement and/or give written notice to the
Purchasers authorizing them to resume sales pursuant to the Registration
Statement. If as a result thereof the prospectus included in the Registration
Statement has been amended to comply with the requirements of the Securities
Act, the Company shall enclose such revised prospectus with the notice to the
Purchasers given pursuant hereto, and the Purchasers shall make no offers or
sales of Registrable Securities pursuant to the Registration Statement other
than by means of such revised prospectus. No more than two such Suspensions, for
a maximum cumulative period of 45 days, shall occur in any 12 month period.

     10. ASSIGNMENT OF REGISTRATION RIGHTS. The rights of the Purchasers
hereunder, including the right to have the Company register Registrable
Securities pursuant to this Agreement, shall be automatically assignable by each
Purchaser to any affiliate of the Purchaser to which all or any portion of the
Registrable Securities are transferred if: (i) the Purchaser agrees in writing
with the transferee or assignee to assign such rights, and a copy of such
agreement is furnished to the Company after such assignment, (ii) the Company is
furnished with written notice of (a) the name and address of such transferee or
assignee, and (b) the securities with respect to which such registration rights
are being transferred or assigned, (iii) the transferee or assignee agrees in
writing for the benefit of the Company to be bound by all of the provisions
contained herein, and (iv) such transfer shall have been made in accordance with
the applicable requirements of the Stock Purchase Agreement and the Warrants, as
applicable.

     11. AMENDMENT OF REGISTRATION RIGHTS. Provisions of this Agreement may be
amended and the observance thereof may be waived (either generally or in a
particular instance and either retroactively or prospectively), only with
written consent of the Company and Purchasers who hold a majority in interest of
the Registrable Securities; provided, however, that no consideration shall be
paid to an Purchaser by the Company in connection with an amendment hereto
unless each Purchaser similarly affected by such amendment receives a pro-rata
amount of consideration from the Company. Unless an Purchaser otherwise agrees,
each amendment hereto must similarly affect each Purchaser. Any amendment or
waiver effected in accordance with this Section 11 shall be binding upon each
Purchaser and the Company.

     12. MISCELLANEOUS.

          (A) A person or entity is deemed to be a holder of Registrable
Securities whenever such person or entity owns of record such Registrable
Securities. If the Company receives conflicting instructions, notices or
elections from two or more persons or entities with respect to the same
Registrable Securities, the Company shall act upon the basis of instructions,
notice or election received from the registered owner of such Registrable
Securities.

          (B) All notices required or permitted hereunder shall be in writing
and shall be deemed effectively given: (i) upon delivery to the party to be
notified, (ii) when received by confirmed facsimile, or (iii) one (1) business
day after deposit with a nationally recognized overnight carrier, specifying
next business day delivery, with written verification of receipt. All
communications shall be sent to the Company and the Purchasers as follows or at
such other


                                      11.

<PAGE>

addresses as the Company or the Purchasers may designate upon ten (10) days'
advance written notice to the other party:

          If to the Company:

               Idera Pharmaceuticals, Inc.
               345 Vassar Street
               Cambridge, MA 02139
               Attn: Chief Executive Officer
               Fax: 617-679-5592

               with a copy simultaneously transmitted by like means to:

               Wilmer Cutler Pickering Hale and Dorr LLP
               60 State Street
               Boston, Massachusetts 02109
               Attn: Stuart Falber
               Fax: (617) 526-5000

     If to a Purchaser, at its address as set forth on the Schedule of
Purchasers attached to the Stock Purchase Agreement.

          (C) Failure of any party to exercise any right or remedy under this
Agreement or otherwise, or delay by a party in exercising such right or remedy,
shall not operate as a waiver thereof.

          (D) This Agreement shall be governed by and construed in accordance
with the laws of the State of New York. The Company and the Purchasers
irrevocably consent to the jurisdiction of the United States federal courts and
the state courts located in the State of New York, Borough of Manhattan, in any
suit or proceeding based on or arising under this Agreement and irrevocably
agree that all claims in respect of such suit or proceeding may be determined in
such courts. The Company and the Purchasers irrevocably waive the defense of an
inconvenient forum to the maintenance of such suit or proceeding. Each party
further agrees that service of process upon such party, mailed by first class
mail, shall be deemed in every respect effective service of process upon such
party in any such suit or proceeding. Nothing herein shall affect the a party's
right to serve process in any other manner permitted by law.

          (E) This Agreement, the Stock Purchase Agreement (including all
schedules and exhibits thereto) and the Warrants constitute the entire agreement
among the parties hereto with respect to the subject matter hereof and thereof.
There are no restrictions, promises, warranties or undertakings, other than
those set forth or referred to herein and therein. This Agreement, the Stock
Purchase Agreement and the Warrants supersede all prior agreements and
understandings among the parties hereto with respect to the subject matter
hereof and thereof.

          (F) Subject to the requirements of Section 10 hereof, this Agreement
shall inure to the benefit of and be binding upon the successors and assigns of
each of the parties hereto.


                                      12.

<PAGE>

          (G) The headings in this Agreement are for convenience of reference
only and shall not limit or otherwise affect the meaning hereof.

          (H) This Agreement may be executed in two or more counterparts, each
of which shall be deemed an original but all of which shall constitute one and
the same agreement. This Agreement, once executed by a party, may be delivered
to the other party hereto by facsimile transmission of a copy of this Agreement
bearing the signature of the party so delivering this Agreement.

          (I) Each party shall do and perform, or cause to be done and
performed, all such further acts and things, and shall execute and deliver all
such other agreements, certificates, instruments and documents, as the other
party may reasonably request in order to carry out the intent and accomplish the
purposes of this Agreement and the consummation of the transactions contemplated
hereby.

          (J) All consents, approvals and other determinations to be made by the
Purchasers pursuant to this Agreement shall be made by the Purchasers holding a
majority in interest of the Registrable Securities (determined as if all shares
of Warrants then outstanding had been converted into or exercised for
Registrable Securities) held by all Purchasers.

          (K) Each party to this Agreement has participated in the negotiation
and drafting of this Agreement. As such, the language used herein shall be
deemed to be the language chosen by the parties hereto to express their mutual
intent, and no rule of strict construction will be applied against any party to
this Agreement.

          (L) For purposes of this Agreement, the term "business day" means any
day other than a Saturday or Sunday or a day on which banking institutions in
the State of New York are authorized or obligated by law, regulation or
executive order to close, and the term "TRADING DAY" means any day on which
AMEX, or if the Common Stock is not then traded on AMEX the principal securities
exchange or trading market where the Common Stock is then listed or traded, is
open for trading.

                  [REMAINDER OF PAGE INTENTIONALLY LEFT BLANK]


                                      13.

<PAGE>

     IN WITNESS WHEREOF, the parties have caused this Agreement to be duly
executed as of the date first above written.

IDERA PHARMACEUTICALS, INC.


By: /s/ Sudhir Agrawal
    ---------------------------------
Name: Sudhir Agrawal
Its: Chief Executive Officer and
     Chief Scientific Officer

                [SIGNATURE PAGE TO REGISTRATION RIGHTS AGREEMENT]

<PAGE>

PURCHASER:

                                        BAKER BROS. INVESTMENTS, L.P.

                                        By: Baker Bros. Capital, L.P.,
                                            its general partner

                                        By: Baker Bros. Capital (GP), LLC,
                                            its general partner


                                        By: /s/ Julian Baker
                                            ------------------------------------
                                        Name: Julian Baker
                                        Title: Managing Member


                                        BAKER BROS. INVESTMENTS II, L.P.

                                        By: Baker Bros. Capital, L.P.,
                                            its general partner

                                        By: Baker Bros. Capital (GP), LLC,
                                            its general partner


                                        By: /s/ Julian Baker
                                            ------------------------------------
                                        Name: Julian Baker
                                        Title: Managing Member

                [SIGNATURE PAGE TO REGISTRATION RIGHTS AGREEMENT]

<PAGE>

PURCHASER:

TANG CAPITAL PARTNERS, LP

By: Tang Capital Management, LLC,
    its General Partner


By: /s/ Kevin C. Tang
    ---------------------------------
    Kevin C. Tang, Manager


                                       2.

<PAGE>

PURCHASER:

FINSBURY EMERGING BIOTECHNOLOGY TRUST
PLC


By: /s/ Samuel D. Isaly
    ---------------------------------
Name: Samuel D. Isaly
Title: Managing Partner of Investment
       Advisor


                                       3.

<PAGE>

PURCHASER:

                                        BAKER BIOTECH FUND I, L.P.

                                        By: Baker Biotech Capital, L.P.,
                                            its general partner

                                        By: Baker Biotech Capital (GP), LLC,
                                            its general partner


                                        By: /s/ Julian Baker
                                            ------------------------------------
                                        Name: Julian Baker
                                        Title: Managing Member


                                        BAKER BIOTECH FUND II, L.P.

                                        By: Baker Biotech Capital II, L.P.,
                                            its general partner

                                        By: Baker Biotech Capital II (GP), LLC,
                                            is general partner


                                        By: /s/ Julian Baker
                                            ------------------------------------
                                        Name: Julian Baker
                                        Title: Managing Member


                                        BAKER BIOTECH FUND II (Z), L.P.

                                        By: Baker Biotech Capital II (Z), L.P.,
                                            its general partner

                                        By: Baker Biotech Capital II (Z) (GP),
                                            LLC, is general partner


                                        By: /s/ Julian Baker
                                            ------------------------------------
                                        Name: Julian Baker
                                        Title: Managing Member


                                        BAKER BIOTECH FUND III, L.P.

                                        By: Baker Biotech Capital III, L.P.,
                                            its general partner

                                        By: Baker Biotech Capital III (GP), LLC,
                                            is general partner


                                        By: /s/ Julian Baker
                                            ------------------------------------
                                        Name: Julian Baker
                                        Title: Managing Member


                                       4.

<PAGE>

PURCHASER:

                                        BAKER BIOTECH FUND III (Z), L.P.

                                        By: Baker Biotech Capital III (Z), L.P.,
                                            its general partner

                                        By: Baker Biotech Capital III (Z) (GP),
                                            LLC, is general partner


                                        By: /s/ Julian Baker
                                            ------------------------------------
                                        Name: Julian Baker
                                        Title: Managing Member


                                        14159, L.P.

                                        By: 14159 Capital, L.P.,
                                            its general partner

                                        By: 14159 Capital (GP), LLC,
                                            is general partner


                                        By: /s/ Julian Baker
                                            ------------------------------------
                                        Name: Julian Baker
                                        Title: Managing Member


                                       5.