We describe here a patient with accelerated phase Philadelphia chromosome (Ph1) negative chronic myelogenous leukemia without BCR gene rearrangement, who received an allogeneic bone marrow transplant following a conditioning regimen consisting of busulfan (BU) and cyclophosphamide (CY). Hematopoiesis was restored following splenectomy performed 1 month post-transplant. There were no distinguishing cytogenetic differences between donor and host. Five years post-transplant the patient relapsed with the original disease. Restriction fragment length polymorphism (RFLP) studies performed at that time exhibited host specific DNA markers suggesting recurrent leukemia of host origin. RFLP analysis of the cells cryopreserved immediately post-transplant also revealed all cells to be of host origin. This patient experienced 5 years of remission with autologous hematopoietic recovery from an aggressive myeloproliferative disorder after high dose BU and CY without engraftment of donor hematopoietic cells.