PURPOSE:This study examines the risk factors for developing perianal abscess or fistula formation after ileal pouch‐anal anastomosis procedure for chronic ulcerative colitis or familial adenomatous polyposis.METHODS:A total of 1,457 patients with J‐pouch, 1,304 (89.5 percent) with chronic ulcerative colitis and 153 (10.5 percent) with familial adenomatous polyposis who had a two‐stage procedure without any evidence of previous perianal disease were included in the study. The effect of pouch‐to‐anal anastomosis type on perianal abscess or fistula formation was evaluated.RESULTS:A total of 108 patients (7.4 percent) had a perianal abscess or fistula after the ileal pouch‐anal anastomosis procedure after at least one year of follow‐up. No statistically significant difference was identified in fistula formation regarding the age and gender of the patients (P>0.05), nor did the risk of fistula formation differ significantly between the patients with handsewnvs.stapled anastomoses (P>0.05). However, patients with a diagnosis of chronic ulcerative colitis, compared with patients with familial adenomatous polyposis, had a statistically higher risk of developing abscess or fistula (P=0.012).CONCLUSION:The most important risk factor in developing perianal sepsis in long‐term patients with ileal pouch‐anal anastomosis is the initial disease type. After excluding patients without Crohn's disease, the risk of developing an abscess or fistula was found to be significantly greater in patients with chronic ulcerative colitis compared with patients with familial adenomatous polyposis, and this risk is independent of anastomotic technique.