In this paper, we report the case of a 19-year-old male patient who presented with lymphoblastic phase of chronic myeloid leukemia and received an allogeneic bone marrow transplant from his cousin. The patient experienced severe, steroid-refractory acute graft versus-host disease of skin, gastrointestinal tract and liver that required further immunosuppression. However, hepatic graft-versus-host disease was complicated with vanishing bile duct syndrome, characterized by progressive destruction of small intrahepatic bile ducts, which was refractory to all available therapies and eventually led to end-stage liver disease. The pathogenesis and treatment of graft-versus-host disease after allogeneic hematopoietic cell transplantation is discussed with an emphasis on liver transplantation for intractable hepatic graft-versus-host disease.