Severe hypoproteinemia often accompanies the development of graft-versus-host disease of the intestine in allogeneic bone marrow transplant patients. To determine whether or not protein loss occurs across the intestinal mucosa in this severe diarrheal illness, we measured fecal alpha 1-antitrypsin once per week in 24-h stool specimens from 25 consecutive patients during hospitalization for bone marrow transplantation. The mean alpha 1-antitrypsin concentration and serum clearance for these patients before transplantation were below 2.6 mg/g stool and 13.0 ml/day (upper limits for normals). Values for all patients increased moderately after pretransplant conditioning. Values for patients who did not develop graft-versus-host disease of the intestine returned to baseline levels; however, those for patients with graft-versus-host disease of the intestine became markedly and persistently elevated (concentration ranged from 16.6 to 51.1 mg/g, clearance from 66.6 to 384.5 ml/day). We conclude that mucosal protein exudation contributes to the hypoproteinemia of graft-versus-host disease of the intestine and that measurement of fecal alpha 1-antitrypsin can be used as a marker for this disease.