This report describes the histological and immunocytochemical findings in gastrointestinal biopsies and skin of a patient with chronic granulocytic leukaemia which progressed to blastic transformation, who was then treated with chemotherapy and total body irradiation followed by allogeneic bone marrow transplantation. The gut showed endocrine cells in the lamina propria and these had an immunophenotype similar to the glandular epithelium at the sites studied (stomach, duodenum and rectum), supporting the idea that the endocrine cells of the gut are more resistant to the effect of radiation, chemotherapy and graft-versus-host disease (GVHD) than are other cell types in the epithelium, and that lamina proprial endocrine cells are epithelially derived in this situation. Epidermis and gut epithelium also showed marked atypia due to the conditioning regimen and GVHD, and this case illustrates the possibility of misdiagnosis of carcinoma in this increasingly common situation. An additional, unusual feature of this case was the presence of a B-cell UCHL1 + ve lymphoma of the colon at autopsy, 122 days post-transplantation.