Intestinal biopsy samples derived from 22 consecutive patients with severe diarrhoea (> 1.5 1/day for 3 or more consecutive days) following allogeneic BMT were analysed for the local presence of cytomegalovirus (CMV) and histological and immunohistological alterations described as typical for acute graft-versus-host disease (GVHD). Seventeen patients showed extensive histopathological lesions typical for acute intestinal GVHD grade > I, 14 marked GVHD-related immunohistological alterations. In intestinal biopsies from 10 of these 22 patients CMV-DNA was detected using PCR- and in situ hybridisation techniques. In 7 of these 10 CMV-DNA positive samples CMV protein expression and in 5 cytomegalic cells were demonstrated. CMV could predominantly be shown in biopsies obtained from the ascending colon and/or the terminal ileum. All 10 patients with local CMV infection showed severe histopathological and immunohistological alterations described as typical for acute intestinal GVHD. Five of seven patients with a CMV-positive intestinal biopsy showed marked improvement of lower gastrointestinal tract disease on antiviral therapy. Five of seven patients lacking local presence of CMV but with severe histopathological lesions responded to therapy with high-dose steroids. Thus, PCR screening for CMV and histopathological analysis may help to treat lower intestinal disease in the marrow transplant recipient early and effectively.