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Background: Outcomes remain controversial for patients undergoing straight (SIAA) vs J pouch (JPAA) ileoanal anastomosis, particularly in children where fewer such cases are performed. Our 3 centers have had extensive experience with both techniques. Thus, we had the unique opportunity to compare outcomes within the same centers., Methods: We retrospectively analyzed 250 children after proctocolectomy with either SIAA or JPAA, for the first 3 years after pull-through. A functional stooling score was developed to further assess outcomes. Data were analyzed using chi(2) tests and generalized linear mixed models for repeated measures., Results: Two hundred three patients had sufficient data for complete analysis (42% males; mean surgery age, 15 +/- 7years). Surgical indications were ulcerative colitis (168) and familial adenomatoid polyposis (35). Surgical procedures included SIAA (112) and JPAA (91). Daytime and nighttime stooling frequencies were significantly higher (P < .013) for SIAA patients at 1 to 24 months after pull-through; however, stooling frequencies began approximating each other by this time. Symptomatic pouchitis (compared to enteritis after SIAA) was significantly higher in JPAA patients (odds ratio, 4.5; confidence interval, 2.32-8.72). Frequency of pouchitis declined with time. There was no significant difference in the incidence of surgical complications between the 2 groups. Finally, continence rates were strikingly good in both groups compared to previously reported series., Conclusion: Straight ileoanal anastomosis and JPAA are associated with considerable morbidity; SIAA has higher stool frequency and JPAA has increased pouchitis. Over time, we found that problems improved, and functional stooling scores became similar. JPAA had consistently lower stool frequency and better continence rates; however, these differences were small and may have minimal clinical significance. In addition, such differences need to be balanced against the high rate of pouchitis with JPAA. Continence was excellent regardless of the technique.