EXHIBIT 23.1


               CONSENT OF ERNST & YOUNG LLP, INDEPENDENT AUDITORS



    We consent to the reference to our firm under the caption "Experts" in the
Amendment No. 1 to the Registration Statement (Form S-3 No. 333-71176) and
related Prospectus of Isis Pharmaceuticals, Inc. and to the incorporation by
reference therein of our report dated February 2, 2001, with respect to the
consolidated financial statements of Isis Pharmaceuticals, Inc. included in its
Annual Report (Form 10-K, as amended on April 2, 2001) for the year ended
December 31, 2000, to be filed with the Securities and Exchange Commission.


                                                  /s/ ERNST & YOUNG LLP

                             ---------------------------------------------------
                                                    ERNST & YOUNG LLP


San Diego, California
October 19, 2001