Restorative proctocolectomy (RP) is generally considered to achieve better results in patients with familial adenomatous polyposis (FAP) than in those with mucosal ulcerative colitis (MUC). We studied 39 pairs of patients (FAP versus MUC), individually matched for surgeon (n = 4), types of ileal pouch (19 S-pouches and 20 J-pouches), technique of ileal pouch-anal anastomosis (21 stapled, 18 handsewn with mucosectomy), duration of follow-up after pouch function (median: 32 months; range: 6 months to 8.5 years), age (median: 30 years; range: 12 to 60 years), and gender (male-to-female ratio: 1.4:1.0). The median duration of operation (3.2 hours), hospital stay (9 days), and the amount of blood loss (about 650 mL) were similar between the two groups. The patients in the MUC group tended to have a higher overall complication rate (28% versus 21%) and more pouch-related septic complications (13% versus 8%, p = 0.6 by chi 2 analysis). Functional results were similar for daytime (median: 5 per day) and nighttime (median: 1 per night) stool frequency and the median duration that defecation could be deferred (median: about 1.5 hours). Perfect continence was present in 34 (87%) patients during the day and in 19 (49%) patients during the night in each group. The use of antidiarrheal medications did not differ between the two groups. According to an analogue scale (from 1 to 10, with 10 being best), the quality of life and health and satisfaction with outcome (median score: 9) were identical between the groups. Thus, in closely matched groups of patients with FAP and MUC, the functional outcome after RP was similar. However, pouchitis was more common in the MUC group (33% versus 10%, p < 0.05 by chi 2 analysis).