Pouchitis is a common complication in patients with ulcerative colitis (UC) following colectomy with ileal pouch-anal anastomosis (IPAA). Recent studies have identified a novel autoantibody against integrin αvβ6 in patients with UC, correlated with disease activity. This study aimed to assess the association between serum anti-integrin αvβ6 antibody levels and pouch inflammation in patients with postoperative UC. Serum anti-integrin αvβ6 antibodies were measured using enzyme-linked immunosorbent assay in patients after IPAA, patients with UC, and controls. We examined sera from 71 subjects, including 28 patients who underwent IPAA, 23 controls, and 20 patients with mild and moderate-to-severe UC. Post-IPAA, patients with UC had higher median anti-integrin αvβ6 levels than that of controls (P<0.001) but lower than that of patients with active UC (P=0.001). Patients with pouchitis had higher antibody levels than those without (P=0.047). The receiver operating characteristics curve for anti-integrin αvβ6 showed an area under the curve of 0.724. The pouchitis activity index endoscopic sub-score was correlated with antibody levels (r= 0.48, P=0.011). Serum anti-integrin αvβ6 antibody levels remain elevated in patients with UC even after total colectomy, and were significantly higher in patients with pouchitis than in those without. This antibody could be a novel and useful biomarker for the diagnosis of pouchitis and assessment of disease activity.