Background. Bone marrow transplantation (BMT) patients frequently develop lifethreatening problems that have similar clinical presentations but differing aetiologies. Despite intensive investigation by haematological, biochemical, and microbiological means, accurate diagnosis is not always possible. Histological and microbiological examination of biopsies from the affected organ may be indicated to enable an accurate diagnosis to be made in these patients. Here we assess the indications, findings, and outcomes in patients who have required surgical biopsy after BMT. Procedure. We retrospectively reviewed all BMT patients who had surgical biopsies between February 1994 and January 1997. Twenty-six patients (1-46 years, median age 10 years) underwent 40 biopsies from the upper and lower GI tract, lung, or liver. Indications for BMT were: relapsed leukaemia = 18; other types of leukae-mia = 3; aplastic anaemia=3; other diseases = 2. Type of BMT: matched related donor = 3, unrelated T-cell depleted donor = 23. Results. Eleven (42%) cases had a change in management; 4 (16%) patients avoided further aggressive therapy because of poor prognosis. Unexpected diagnoses were found in 7 biopsies: 1 acute colitis, 1 duodenal ulcer, 1 liver aspergilloma, 2 transfusion siderosis, 1 radiation fibrosis of the lung, and 1 cytomegalovirus infection of the lung. Three patients were noted to have complications after their procedure. Conclusions. Surgical biopsies for undiagnosed prob- lems can be of benefit in the management of very sick patients who have received bone marrow transplantations. Despite the fact that these patients are so unwell, there is a low rate of complications related to surgery and anaesthesia.