The immediate postoperative and long-term functional results of 51 ulcerative colitis patients and 21 familial polyposis patients who underwent ileal J-pouch-anal anastomosis were compared in this study. The incidence of postoperative complications requiring reoperation was not statistically different in both groups. The mean daily stool frequency was significantly higher in colitis patients. Pouchitis occurred in 44% of colitis patients but not in polyposis patients (P < 0.005). Symptoms of pouchitis included bloody diarrhea, urgency, abdominal pain, weight loss, fever, and arthritis. Six colitis patients required pouch excision because of intractable pouchitis. The overall pouch excision rate was 22% in ulcerative colitis patients and 5% in familial polyposis patients. Patient satisfaction was good in 46% of ulcerative colitis patients and 76% of polyposis patients (P < 0.05). Our data demonstrate that the long-term outcome of ileal pouch-anal anastomosis is more favorable in polyposis patients than in colitis patients. Pouchitis is a major long-term complication occurring exclusively in colitis patients.