A 21-year-old female underwent allogeneic bone marrow transplantation (ABMT) from her HLA matched brother for chronic myeloid leukaemia in the chronic phase. Four weeks post transplant she developed tenesmus, mucoid stool mixed with blood and lower abdominal pain. This rapidly progressed to greenish watery diarrhoea with flakes of mucous membrane floating in it, conforming to the classical clinical description of acute GVHD of the bowel. Stool microscopy showed profuse numbers of Blastocystis hominis, a parasite with doubtful pathogenicity in an immunocompetent host. In the present case the parasite played a pathogenic role as evidenced by the profuse number in the stool sample, focal neutrophil infiltration of the rectal mucosa, initial presentation of the patient with dysentery, and requirement for prolonged metronidazole therapy to eradicate the parasite and cure the diarrhoea. She also had grade I GVHD of the liver and skin. In developing tropical countries, hitherto unreported parasitic infestations may complicate the picture of acute GVHD.