A patient with non-Hodgkin's lymphoma in remission developed a myelodysplastic syndrome (MDS) 12 years after ABMT. This patient had undergone bone marrow harvesting prior to any chemoradiotherapy. He had received the autograft following conditioning with high-dose CY and TBI. Chromosomal analysis of BM cells revealed complicated abnormalities. Similar karyotypic abnormalities in host-derived BM cells were found in another patient with AML who had received allogeneic BM following conditioning with CY plus TBI 15 months previously. These findings suggest that MDS or clonal karyotypic abnormalities following ABMT may derive from endogenous hematopoietic stem cells that survive the BMT preparative regimen.