We undertook a retrospective review of all 76 patients with AML transplanted between August 1986 and March 1995 at our center. All patients received melphalan (140–160 mg/m2), etoposide (60 mg/kg) and total body irradiation. All patients had bone marrow cytogenetic analysis at regular intervals following ABMT. The primary study end point was the development of the new cytogenetic abnormalities. Secondary end points were the development of myelodysplasia (MDS) or AML. Sixty-two of 77 patients were alive at least 6 months post transplant. Cytogenetic abnormalities developed in 7/62 patients (11%) following ABMT. No patients demonstrated MDS or AML. At a median of 30 months after development of the cytogenetic abnormality, only one patient developed features suggestive but not diagnostic of MDS. All seven patients remain alive and leukemia-free up to 70 months after detection of the abnormal clone. There was no increased incidence of cytogenetic abnormalities developing in patients receiving a purged autograft. New cytogenetic abnormalities are frequent following ABMT for AML but do not appear to predict development of myelodysplasia or acute myeloid leukemia. These abnormalities may relate to use of total body radiation as part of the high-dose therapy.