The aim of this study was to compare the immediate postoperative results and the long-term outcome of ileal pouch-anal anastomosis in 94 patients with familial adenomatous polyposis to those in 758 patients with ulcerative colitis. Two colitis patients died after operation (0.3%), but no polyposis patients died. Overall operative complications appeared in 26% and 29% of polyposis and colitis patients, respectively (NS). Reoperation for intestinal obstruction did not differ between the two groups, but sepsis requiring reoperation was more common in colitis patients (6%) than in polyposis patients (0%, p < 0.04). At follow-up (mean, 3 years), polyposis patients had fewer daytime stools (4.5 stools per day), less nighttime fecal spotting (26%), and less pouchitis (7%) than colitis patients (5.8 stools per day; spotting, 40%; pouchitis, 22%; p < 0.002). The conclusion was that polyposis patients tolerated the operation better and had less long-term disability than did colitis patients. The data suggest that postoperative sepsis, daytime stooling frequency, nocturnal incontinence, and pouchitis may be, at least in part, disease related and not surgeon or operation related.