A 28-year-old man with acute promyelocytic leukemia at first early relapse received HLA-matched allogenic bone marrow transplantation (BMT) at first early relapse. Cyclosporin A and methotrexate were administered at conventional doses as a prophylaxis for graft-versus-host disease (GVHD). He presented with severe bloody diarrhea on day 87 after BMT. Examination of the lower gastrointestinal tract revealed diffuse mucosal change of inflammation. A diagnosis of late onset of acute gut GVHD was made, in the absence of other manifestations such as skin and liver involvement. A further survey is needed to clarify the incidence and the pathogenesis of atypical gut GVHD.