A prospective study was conducted to determine the implications of acute pouchitis on the long-term functional results of restorative proctocolectomy with J-pouch ileoanal anastomosis (IPAA). Between July 1988 and June 1996, 137 consecutive patients underwent IPAA for treatment of ulcerative colitis. 127 patients (93%) have been available for follow-up. All patients completed diaries detailing bowel habits over a 7-day period at 3, 6, 9, 12, 18, 24 months, and yearly after reestablishment of intestinal continuity. Diaries were completed only during time periods in which patients were not suffering from acute symptomatic pouchitis. Patients with chronic pouchitis (n = 7) were excluded from this study leaving 120 patients for analysis. Fifty patients suffered at least one episode of pouchitis (Pouchitis Group). Seventy patients never had pouchitis (No Pouchitis Group). Patients with a history of pouchitis having significantly more bowel movements per day were more likely to ever have minor incontinence (75% vs. 45%, p < 0.005) or major incontinence (37% vs. 17%, p < 0.02). The stools of Pouchitis Group were less likely to be formed (24% vs. 31%, p < 0.001). Pouchitis Group patients also were more likely to wear a protective pad during the day (21% vs. 7% p < 0.04) or during the night (40% vs. 13%, p < 0.001). Even in the absence of clinically active pouchitis, patients who have suffered at least one episode of pouchitis have a poorer long-term functional result after IPAA. The results of this study suggest that ileal pouchitis may represent a chronic condition that displays episodic symptomatic exacerbations.