BACKGROUND: Graft-versus-host disease (GVHD) is an important cause of morbidity and mortality after allogeneic bone marrow transplantation (BMT). The clinical diagnosis of gastrointestinal GVHD can be difficult to establish and endoscopic diagnosis entails a procedural risk. The aim of this study was to determine whether rectal biopsy alone might be sufficient to establish or exclude the diagnosis of intestinal GVHD. METHODS: A retrospective chart review of children with histological evidence of gastrointestinal GVHD after allogeneic BMT at the Royal Children's Hospital in Melbourne, Australia, between January 1981 and July 2004. RESULTS: During the study period, 264 patients received allogeneic BMT. Thirty-three had either an upper or lower gastrointestinal endoscopy, or both. Of these, 14 (8 M: 6 F, mean age 9 years 5 months at the time of BMT) had histological features suggestive of GVHD in at least one gastrointestinal biopsy. Overall, 9 of 14 could have been diagnosed with GVHD on the basis of rectal biopsies alone (negative predictive value: 64%). Gastroscopy was needed to establish the diagnosis in a further five patients. Multiple biopsies obtained from each site in the lower gastrointestinal tract showed similar histological findings, but there was frequent non-agreement between biopsies obtained at differing sites within the upper gastrointestinal tract. CONCLUSIONS: Based on these results, we suggest that regardless of symptoms, rectal biopsy should initially be performed to identify gastrointestinal GVHD. Gastroscopy should be added only if the rectal biopsy is unhelpful and there is still good reason to suspect GVHD.