OBJECTIVE To investigate the role of faecal alpha 1-antitrypsin concentration in the diagnosis and management of patients with ileal pouch-anal anastomosis. DESIGN Prospective study. METHODS Fifty-two measurements of faecal alpha 1-antitrypsin concentration were taken from 33 patients operated on for ulcerative colitis. RESULTS Patients with active pouchitis (44.4 +/- 7.1 mg%) had a three-fold higher mean faecal alpha 1-antitrypsin concentration than patients in remission (13.7 +/- 1.3 mg%; P < 0.0001), than patients who had never had pouchitis (14.4 +/- 2.3 mg%; P < 0.003) and than patients with incontinent ileostomies (12.7 +/- 1.3 mg%; P < 0.004). Faecal alpha 1-antitrypsin measurements were 80% sensitive and 97% specific for active pouchitis. A significant positive correlation between the pouchitis disease activity index and faecal protein loss was observed (r = 0.702; P < 0.0001). The correlations between protein loss and other parameters were weaker (protein loss versus clinical score, r = 0.309; versus endoscopic score, r = 0.583; and versus histologic score, r = 0.558). CONCLUSION Faecal alpha 1-antitrypsin concentration is a good indicator of the degree of intestinal inflammation in pouchitis and may be useful as a quantitative index of disease activity in prospective studies.