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This study was designed to determine the incidence of persistent perineal sinus after pouch excision in inflammatory bowel disease, risk factors, and long-term clinical course.The study included 35 consecutive patients who underwent pouch excision at St. Mark's Hospital, London, between 1996 and 2006. Incidence of persistent perineal sinus and its long-term clinical course were reported. Sixteen variables were analyzed to determine their association with persistent perineal sinus.There were 17 men and 18 women with median age of 37 (range, 20-57) years. The final diagnosis was ulcerative colitis in 28 and Crohn's disease in 7 patients. The indications for pouch excision included pelvic or perineal sepsis in 60 percent, pouchitis in 23 percent, and poor pouch function in 17 percent. Persistent perineal sinus was diagnosed in 14 patients (40 percent). Pouch excision for fistula or abscess in the pelvis or perineum (odds ratio, 8; 95 percent confidence interval, 1.4-45.5) was an independent predictor for persistent perineal sinus. Twenty-six procedures were performed in patients with persistent perineal sinus and resulted in healing in 64 percent. Curettage was the most common procedure used.Pouch excision for pelvic or perineal sepsis was an independent predictor for persistent perineal sinus.