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CORRESPONDENCE

[BioCryst Letterhead]

Mr. Jim Rosenberg

Senior Assistant Chief Accountant

Division of Corporation Finance

U.S. Securities & Exchange Commission

100 F Street, NW

Washington, DC 20001-2016

    Re:

    BioCryst Pharmaceuticals, Inc.

Form 10-K for the Fiscal Year Ended December 31, 2007

File No. 0-23186; Form 10-Q for the Quarter Ended March 31, 2008;
Form 10-Q for
the Quarter Ended June 30, 2008

Dear Mr. Rosenberg:

This letter responds to your letter dated October 31, 2008 in connection with the above referenced
file. To facilitate your review, we have reproduced your comments in bold below and have provided
our response immediately following your comment.

Form 10-K for the Fiscal Year Ended December 31, 2007

    1.

    We note your response to our prior comment 1 and the proposed changes to the
disclosure that will be included in future filings. Please expand your disclosure to also
discuss the following information:

    •

    In your discussion of the Mundipharma corporate alliance, please disclose the
percentage range of royalties (i.e., single digits, low teens, high teens, etc.).

    •

    In your discussion of the AECOM and IRL academic alliance, please disclose the
aggregate potential milestone payments, the annual license
fee, the percentage range of royalties on future sales of any resulting product, and
each party’s other rights and obligations.

    •

    In your discussions of the UAB and Emory academic alliances, please disclose the
percentage range of royalties.

In response to your comment, we have further revised our disclosure and have included the
information you requested above. Exhibit A is a sample of our revised disclosure, which
has been redlined for convenience to show the information added since our last Form 10-K filing.

Form 10-Q for the quarter ended June 30, 2008

    2.

    We noted your response to our comment 8. Please tell us how you are accounting for
the remaining portion of the revenue related to this contract (HHS). It would appear that
the company’s ability to estimate revenues related to the remaining portion of the HHS
contract would be diminished as a result of HHS’s change in reimbursable costs structure.

The Company’s contract with HHS is a cost-plus-fixed-fee contract. That is, we are entitled to
receive reimbursement for all reasonable and allowable costs incurred in accordance with the
contract provisions that are related to the development of peramivir plus a fixed fee, or profit.
As outlined in Staff Accounting Bulletin No. 104, Revenue Recognition, and Accounting Research
Bulletin No. 43, Chapter 11, Section A, Government Contracts, Cost-Plus-Fixed-Fee Contracts, the
Company has and continues to recognize revenue as reimbursable costs are incurred under the
contract with HHS. The Company does not estimate revenues based on percentage of contract
completion or any other method of revenue recognition.

As disclosed in our initial response, the Company announced in January 2008 that the development
plan for peramivir had changed and that HHS would only fund certain elements of the revised
program. This decision by HHS did not change or alter the reimbursable cost structure of the
Company’s contract or the Company’s accounting related to the contract. The Company is currently
executing the development plan for peramivir that has been approved by HHS. We will only recognize
revenue related to this approved development plan and only up to the specified limits of the
contract. We have not recognized revenue in excess of the contract amount of $102.6 million.

*          *          *

The Company acknowledges that it is responsible for the adequacy and accuracy of the disclosure in
the filing; staff comments or changes to disclosure in response to staff
comments do not foreclose the Commission from taking any action with respect to the filing; and the
Company may not assert staff comments as a defense in any proceeding initiated by the Commission or
any person under the federal securities laws of the United States.

If you have any questions, please contact our outside corporate counsel, Brian Lane of Gibson, Dunn
& Crutcher LLP at (202) 887-3646.

Sincerely,

/s/ Stuart Grant

Stuart Grant

Senior Vice President & Chief Financial Officer

    Cc:

    Jon Stonehouse

Mike Darwin

Alane Barnes

Brian Lane

Mike Mills

EXHIBIT A

Collaboration and In-License Relationships

     We seek to enter into collaborations with leading pharmaceutical and biotechnology companies
when we feel it is advantageous to leverage these companies’ resources to develop and commercialize
our drug candidates on a global basis. This allows us to remain focused on our strength of early
stage discovery and development of drug candidates. To date, we have two major collaborations for
the development and commercialization of our lead PNP inhibitors and two collaborations for the
development and commercialization of peramivir in certain countries outside the U.S. In addition,
in January 2007, we announced that HHS had awarded the Company a $102.6 million, four-year contract
for the advanced development of peramivir for U.S. licensure.

     Another important component of our strategy is to augment our internal discovery programs through
the selective in-licensing of potential drug development targets or early stage compounds for these
specific targets. For example, our PNP inhibitors were in-licensed from AECOM and IRL in June 2000.

Corporate Alliances

     Roche. In November 2005, we entered into an exclusive license with Roche for the development
and commercialization of our second generation PNP inhibitor, BCX-4208, for the prevention of acute
rejection in transplantation and for the treatment of autoimmune diseases. Under the terms of the
agreement, Roche obtained worldwide rights to BCX-4208 in exchange for an up-front payment of $30
million, which included a payment as reimbursement for a limited supply of material during the
first 24 months of the collaboration. The license also provided for future milestone event payments
for achieving specified development, regulatory and commercial milestones (including sales level
milestones following a product’s launch) for certain indications. In addition, the license provided
for the Company to receive royalties based on a percentage of net product sales, which varies
depending upon when certain indications receive New Drug Application (“NDA”) approval in a major
market country and can vary by country depending on the patent coverage or sales of generic
compounds in a particular country. We licensed this compound and other PNP inhibitors from AECOM
and IRL and will owe sublicense payments to these third parties on any upfront payment, future
event payments and royalties received by us for the sublicense of these inhibitors.

     Roche has a right of first negotiation, under certain conditions, on existing backup PNP
inhibitors we develop through Phase IIb in transplant rejection and autoimmune diseases, but any
new PNP inhibitors are exempt from this agreement and we retain all rights to such compounds. We
retain the right to co-promote BCX-4208 in the U.S. for certain indications. Roche has certain
obligations under the terms of the agreement to use commercially reasonable efforts to develop,
manufacture and commercialize the licensed product. The agreement may be terminated by either party
following an uncured material breach by the other party or may be either fully or partially
terminated by Roche without cause under certain conditions and all rights, data, materials,
products and other information would be transferred to the Company. For termination without cause,
the effective date of termination is 180 days from the date of notice.

     In May 2008 the Company received notice that Roche was exercising the “no cause” termination
right under the license agreement for BCX-4208. Upon termination, the Company will recognize the
remaining deferred revenue and deferred expense related to the license agreement, which are $27.3
million and $8.4 million, respectively, as of March 31, 2008.

     Mundipharma. In February 2006, the Company entered into an exclusive, royalty bearing right
and license in the specified territory (primarily Europe, Asia and Australia) with Mundipharma for
the development and commercialization of our lead PNP inhibitor, forodesine HCl, for use in
oncology. Under the terms of the agreement, Mundipharma obtained oncology rights to forodesine HCl
in the specified territory in exchange for a $10 million up-front payment. Mundipharma will share
50% of the documented third party development costs incurred by us in respect of our current and
planned trials as of the effective date of the agreement provided that Mundipharma’s maximum
contribution to these trials shall be $10 million. In addition, Mundipharma will conduct
additional clinical trials at their own cost up to a maximum of

$15 million. The license provides
for possibility of future event payments totaling $155 million for achieving specified development,
regulatory and commercial events (including certain sales level amounts following a product’s
launch) for certain indications. In addition, the agreement provides that we will receive
royalties (ranging from single digits to mid teens) based on a percentage of net product sales,
which varies depending upon when certain indications receive NDA approval in a major market country
and can vary by country depending on the patent coverage or sales of generic compounds in a
particular country. Generally, all payments under the agreement are nonrefundable and
non-creditable, but they are subject to audit. We licensed this compound and other PNP inhibitors
from AECOM and IRL and will owe sublicense payments to these third parties on the upfront payment,
future event payments and royalties received by us for the sublicense of these inhibitors.

     Within five years of the effective date of the agreement, Mundipharma has a right of first
negotiation on existing backup PNP inhibitors we develop through Phase IIb in oncology, but any new
PNP inhibitors are exempt from this agreement and we retain all rights to such compounds. We retain
the rights to forodesine HCl in the U.S. and Mundipharma is obligated by the terms of the agreement
to use commercially reasonable efforts to develop the licensed product in the territory specified
by the agreement. The agreement will continue for the commercial life of the licensed products, but
may be terminated by either party following an uncured material breach by the other party or in the
event the pre-existing third party license with AECOM and IRL expires. It may be terminated by
Mundipharma upon 60 days written notice without cause or under certain other conditions as
specified in the agreement and all rights, data, materials, products and other information would be
transferred to us at no cost. In the event we terminate the agreement for material default or
insolvency, we could have to pay Mundipharma 50% of the costs of any independent data owned by
Mundipharma in accordance with the terms of the agreement.

     Shionogi. In March 2007, the Company entered into an exclusive license agreement with Shionogi
to develop and commercialize the Company’s lead influenza neuraminidase inhibitor, peramivir, in
Japan for the treatment of seasonal and potentially life-threatening human influenza. Under the
terms of the agreement, Shionogi obtained rights to injectable formulations of peramivir in Japan
in exchange for a $14 million up-front payment. The license provides for potential future milestone
event payments (up to $21 million) and commercial event milestone payments (up to $95 million) in
addition to double digit (between 10 and 20% range) royalty payments on product sales of peramivir.
In December 2007, the Company received a $7 million milestone payment from Shionogi for their
initiation of a Phase II clinical trial with i.v. peramivir. Generally, all payments under the
agreement are nonrefundable and non-creditable, but they are subject to audit. Shionogi will be
responsible for all development, regulatory and marketing costs in Japan. The term of the
agreement is from February 28, 2007 until terminated by either party in accordance with the license
agreement. Either party may terminate in the event of an uncured breach. Shionogi has the right
of without cause termination. In the event of termination all license and rights granted to
Shionogi shall terminate and shall revert back to the Company. The Company developed peramivir
under a license from UAB and will owe sublicense payments to them on the upfront payment and any
future event payments and/or royalties received by the Company from Shionogi. The Company retains
all rights to commercialize peramivir in North America, Europe, and other countries outside of
Korea and Japan.

     Green Cross Corporation (“Green Cross”). In June 2006, the Company entered into an agreement
with Green Cross to develop and commercialize peramivir in Korea. Under the terms of the agreement,
Green Cross will be responsible for all development, regulatory, and commercialization costs in
Korea. The Company received a one-time license fee of $250,000. Total future milestone payments
would be equally modest. The license also provides that the Company will share in profits
resulting from the sale of peramivir in Korea, including the sale of peramivir to the Korean
government for stockpiling purposes. Furthermore, Green Cross will pay the Company a premium over
its cost to supply peramivir for development and any future marketing of peramivir products in
Korea. Both parties have the right to terminate in the event of an uncured material breach. In the
event of termination all rights, data, materials, products and other information would be
transferred to the Company.

Academic Alliances     Albert Einstein College of Medicine of Yeshiva University and Industrial Research, Ltd, New
Zealand. In June 2000, we licensed a series of potent inhibitors of PNP from AECOM and IRL. The
lead drug candidates from this collaboration are forodesine HCl and BCX-4208. We have obtained
worldwide exclusive rights to develop and ultimately distribute these compounds or any other drug
candidates that might arise from research on these inhibitors. We have the option to expand the
Agreement to include other inventions in the field made by the investigators or employees of AECOM
and IRL. We have agreed to use commercially reasonable efforts to develop these drugs. In
addition, we have agreed to pay certain milestone payments for each licensed product (which range
in the aggregate from $1.4 million to almost $4 million per indication) for future development of
these inhibitors, single digit royalties on net sales of any resulting product made by us, and to
share approximately one quarter of future payments received from other third-party partners, if
any. In addition, we have agreed to pay annual license fees which can range from $150,000 to
$500,000 depending on stage of development of products that is non-refundable, but is creditable
against actual royalties and other payments due to AECOM and IRL. This agreement may be terminated
by us at any time by giving 60 days advance notice or in the event of material uncured breach by
AECOM and/or IRL.

     The University of Alabama at Birmingham. We have had a close relationship with UAB since our
formation. Our former Chairman, Dr. Charles E. Bugg, was the previous Director of the UAB Center
for Macromolecular Crystallography, and our Chief Operating Officer, Dr. J. Claude Bennett, was the
former President of UAB, the former Chairman of the Department of Medicine at UAB and a former
Chairman of the Department of Microbiology at UAB. Several of our early programs originated at UAB.

     We currently have agreements with UAB for influenza neuraminidase and comple