We describe a pattern of relapse in 601 patients who received an allogeneic hematopoietic stem cell transplant at our institution for acute or chronic leukemia and myelodysplasia over a period of 18 years. We show a correlation between chronic graft-versus-host disease and extramedullary relapse, suggesting that the expected graft versus leukemia effect in patients with chronic graft-versus-host disease may preferentially maintain marrow remission without preventing relapse in extramedullary sites.