BACKGROUND: Therapy options for mesalamine-refractory ulcerative colitis (UC) include immunosuppressive medications or surgery. Chronic immunosuppressive therapy increases risks of infection and cancer, whereas surgery produces a permanent change in bowel function. We sought to quantify the willingness of patients with UC to accept the risks of chronic immunosuppression to avoid colectomy. METHODS: We conducted a state-of-the-art discrete-choice experiment among 293 patients with UC who were offered a choice of medication or surgical treatments with different features. Random parameters logit was used to estimate patients' willingness to accept trade-offs among treatment features in selecting surgery versus medical treatment. RESULTS: A desire to avoid surgery and the surgery type (ostomy versus J-pouch) influenced patients' choices more than a specified range of 10-year mortality risks from lymphoma or infection, or disease activity (mild versus remission). To avoid an ostomy, patients were willing to accept a >5% 10-year risk of dying from lymphoma or infection from medical therapy, regardless of medication efficacy. However, data on patients' stated choice indicated perceived equivalence between J-pouch surgery and incompletely effective medical therapy. Patient characteristics and disease history influenced patients' preferences regarding surgery versus medical therapy. CONCLUSIONS: Patients with UC are willing to accept relatively high risks of fatal complications from medical therapy to avoid a permanent ostomy and to achieve durable clinical remission. However, patients view J-pouch surgery, but not permanent ileostomy, as an acceptable therapy for refractory UC in which medical therapy is unable to induce a durable remission.