EXHIBIT 23.1 CONSENT OF ERNST & YOUNG LLP, INDEPENDENT AUDITORS We consent to the incorporation by reference in the Registration Statements on Form S-8 (No.'s 333-107416, 333-87266, 333-64238, 333-63950, 333-44852, 333-87759, 333-62437, 333-11577, 333-96302, 333-81236, and 333-44336) and Form S-3 (No.'s 333-109641 and 333-76544) of our report dated February 20, 2004 (except for the first paragraph to Note 7 and Note 11, as to which the date is March 29, 2004), with respect to the consolidated financial statements of Epimmune, Inc. included in the Annual Report (Form 10-K) for the year ended December 31, 2003. San Diego, California March 26, 2004