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Pouchitis is a major problem after ileal pouch–anal anastomosis in patients with ulcerative colitis. Chronic pouchitis is particularly troublesome. This study aimed to identify risk factors for the development of chronic pouchitis in a Japanese population.We retrospectively reviewed 100 patients who underwent pouchoscopy for a functioning ileal pouch. The diagnosis of pouchitis was made according to the modified pouchitis disease activity index. The incidence of pouchitis was estimated using the Kaplan–Meier curve, and Cox regression analysis was used to identify risk factors for the development of chronic pouchitis.Twenty-two patients developed pouchitis; 12 of them had chronic pouchitis. The incidences of chronic pouchitis were 3.3%, 7.6%, and 16.6% at 2, 5, and 10 years, respectively, after the pouch operation. The incidence of pouchitis was significantly higher in patients with preoperative extraintestinal manifestations (EIMs) than in those without (log-rank test, P = 0.002 and P = 0.005 for overall and chronic pouchitis, respectively). Cox regression analysis revealed that the presence of extraintestinal manifestations was an independent risk factor for the development of overall (hazard ratio: 4.48, 95% confidence interval, 1.77–11.30, P = 0.002) and chronic (hazard ratio: 5.81, 95% confidence interval, 1.67–20.23, P = 0.006) pouchitis.The presence of preoperative extraintestinal manifestations was found to be an independent risk factor for the development of overall and chronic pouchitis.