We report a case of severe hemorrhagic cystitis complicating high-dose cyclophosphamide (CY), total body irradiation and allogeneic hematopoietic stem cell transplantation (HSCT). Supportive care with i.v. hydration, platelet transfusions, continuous bladder irrigation and aluminum irrigation of the bladder was ineffective and the patient developed multiple complications from hemorrhagic cystitis. His condition became critical with persistent bleeding, pulmonary edema and acute renal failure. These problems resolved following successful simple cystectomy and ileal conduit. The patient did not develop any acute or chronic complications following surgery. He is alive with a good quality of life and in third remission after receiving salvage chemotherapy 14 months after his transplantation.