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Purpose: The outcome of ileal pouch-anal anastomosis in patients with backwash ileitis is controversial. We prospectively compared the outcomes of ileal pouch-anal anastomosis in colitis patients with backwash ileitis and colitis patients without backwash ileitis., Methods: Consecutive colitis patients undergoing ileal pouch-anal anastomosis were reviewed. All patients were classified after surgery as being either backwash ileitis-positive or backwash ileitis-negative. Serum drawn preoperatively was assayed, using enzyme-linked immunosorbent assay, for anti-Saccharomyces cerevisiae, anti-outer membrane of porin C, anti-CBir1, anti-I2, and perinuclear anti-neutrophil cytoplasmic antibody. Outcomes included acute pouchitis (antibiotic responsive), chronic pouchitis (antibiotic dependent or refractory), or de novo Crohn's disease (small inflammation above the pouch inlet or pouch fistula)., Results: Out of 334 patients, 39 (12%) were backwash ileitis-positive. Compared with backwash ileitis-negative patients, backwash ileitis-positive patients had a higher incidence of pancolitis (100% vs 74%; P = .0001), primary sclerosing cholangitis (15% vs 2%; P = .001) and high-level (>100 enzyme-linked immunosorbent assay units/ml) perinuclear anti-neutrophil cytoplasmic antibody expression (29% vs 9%; P = .001). After a median follow-up of 26 months, 53 patients (16%) developed acute pouchitis, 37 (11%) developed chronic pouchitis, and 40 (12%) developed de novo Crohn's disease. There was no significant difference between the backwash ileitis-positive and backwash ileitis-negative patient groups in the incidence of acute pouchitis, chronic pouchitis, or de novo Crohn's disease., Conclusion: There was a significantly higher incidence of pancolitis, primary sclerosing cholangitis, and high-level perinuclear anti-neutrophil cytoplasmic antibody expression in backwash ileitis-positive patients than in backwash ileitis-negative patients. The incidence of acute pouchitis, chronic pouchitis, and de novo Crohn's disease after ileal pouch-anal anastomosis does not differ significantly between backwash ileitis-positive and backwash ileitis-negative patients.