EXHIBIT 16.1 [DELOITTE & TOUCHE LETTERHEAD] August 25, 2004 Securities and Exchange Commission Mail Stop 11-3 450 5th Street, N.W. Washington, D.C. 20549 Dear Sirs/Madams: We have read Item 4 of Ligand Pharmaceuticals Incorporated's Form 8-K/A dated August 25, 2004, and we agree with the statements made in sentences 1, 2 and 3 of the first paragraph and the statements in paragraphs 2, 3 and 4. We have no basis to agree or disagree with the 4th sentence in paragraph 1. Yours truly, /s/ Deloitte & Touche LLP