EXHIBIT 99.1

                              [Ligand Letterhead]

October 3, 2005

Daniel S. Loeb
Chief Executive Officer
THIRD POINT LLC
390 Park Avenue
New York, NY 10022

Dear Mr. Loeb:

I am in receipt of your letters dated September 23, 2005 and September 30, 2005,
and have discussed them with the Board of Directors of the Company.

As you know, and as I expect was your intention in publishing these letters, the
Company cannot respond substantively to your one-sided perspective on the
Company's performance and value due to its current reporting position. As soon
as the Company releases its restated results and its 2005 periodic reports are
current, management plans to provide a full business update and to spend
significant time with stockholders, whether one-on-one or in investor meetings.
However, as to the procedural matters you have raised in your most recent
letter:

1. The Audit Committee, the Board of Directors and management, as well as the
outside auditors, have been, and continue to be, intensely focused on completing
the Company's previously announced restatement as promptly as possible. The
Company's highest priority is to become current on its public information by
completing the restatement and filing the Company's amended historical restated
annual financial statements and 2005 periodic reports. Subject to acceptance of
a mutually agreed upon written confidentiality agreement, the Company would be
willing to meet with you to discuss the status of that process and resources
devoted, and consider any suggestion you might have to further accelerate that
process.

2. The Company has referred your request to increase the trigger threshold to
20% or rescind the Company's shareholder rights plan to the independent
directors under the coordination of the Board's lead independent director, John
Groom. They will, I know, consider your request carefully and in the context of
their duties to all stockholders.

3. As to your requests for appointment of directors, our Nominating Committee
will await your presentation of candidates for our Board of Directors. It will
consider those candidates' credentials and interests promptly along with other
potential candidates that have been and might be considered as part of the
Nominating Committee's normal process. Following this process, the Nominating
Committee will make a recommendation to the Board whether such candidates merit
appointment now, or whether you should instead submit them to our stockholders
directly in connection with our next annual meeting.




4. We are equally desirous of conducting our annual meeting expeditiously, and
are prepared to discuss with you a mutually agreeable date for that meeting
which allows our stockholders adequate time to consider the Company's financial
position and business update following release of our restated results and our
2005 periodic reports, so that all of the Company's stockholders are able to
have an understanding of the Company's business, financial condition, results of
operations and liquidity.

To facilitate the continued focus of the Audit Committee, the Board of Directors
and management on completion of the restatement process, John Groom and I will
serve as your point of contact with the Board on a going forward basis. This
will allow the other members of the Board of Directors, particularly the members
of the Board's Audit Committee, to focus their efforts on completing the
restatement of the Company's historical financial statements.

John and I look forward to having a more balanced dialogue related to your
proposals and to continuing to build the value of the Company's assets - value
which has been built over the last 10 to 15 years by the Company's current
management team.

Best regards,

/s/ David E. Robinson

David E. Robinson

Chairman, President and Chief Executive
Ligand Pharmaceuticals Incorporated

cc:      Board of Directors of Ligand Pharmaceuticals Incorporated