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Predictive factors for the development of pouchitis after ileal pouch-anal anastomosis (IPAA) in children have not been well studied. In this retrospective study, the incidence and risk factors that predict pouchitis in children with IPAA will be identified.The records of patients who underwent IPAA surgery at Children's Hospital of Wisconsin between January 2000 and December 2013 were reviewed retrospectively. Patients with clinical, endoscopic, and histological findings consistent with pouchitis were identified. The groups of patients with and without pouchitis or chronic pouchitis were compared to determine which demographic, pathological, or disease characteristics may serve as predictive factors for the development of pouchitis or chronic pouchitis.Out of a total of 60 patients who underwent IPAA, preoperative diagnosis was ulcerative colitis (UC) in 43 and familial adenomatous polyposis (FAP) in 17. Pouchitis was identified in 24 (56%) patients with UC and 2 (12%) patients with FAP. Subgroup analysis of patients with UC revealed that chronic pouchitis occurred in 15 (35%) patients. The median follow-up period from construction of the IPAA was 35 months (range 4.59–104.26 months). The study analysis revealed that a higher Pediatric Ulcerative Colitis Activity Index score at the time of diagnosis was a significant predictive factor for both pouchitis (P = 0.001) and chronic pouchitis (P = 0.02).Patients with UC and a higher PUCAI score at the time of diagnosis have a higher risk for developing pouchitis.