A 46-year-old man who had been treated with azathioprine (150 mg/day) and prednisolone (7.5-10 mg/day) for 16 years after allogeneic renal transplantation was admitted to our hospital in July 1996 for evaluation of pancytopenia. Three years earlier he had been given a diagnosis of renal pelvic and ureteral cancer, and underwent left nephrectomy with total uretectomy. His bone marrow was normocellular with excess of blasts (27.6%), and displayed trilineage myelodysplasia. A chromosomal analysis of the bone marrow revealed 43-45, XY with del (1) (p13), -5, del (7) (q22), -17, -18, and -19. The patient was given a diagnosis of refractory anemia with excess of blasts in transformation (RAEB in T), and treated with idarubicin and cytosine arabinoside. Two months later, overt acute leukemia developed and reinduction chemotherpay was started, but the patient died of cerebral hemorrhage in October. This case suggests that immunosuppressive agents such as azathioprine might play an important role in the pathogenesis of MDS (RAEB in T) and renal pelvic and ureteral cancer after renal transplantation.