The presentation cytogenetic result was correlated with outcome for 999 patients with acute myeloblastic leukemia (AML) having bone marrow transplantation (BMT) in first complete remission (CR1). The karyotype at diagnosis was classified according to the modified Chicago classification. Allogeneic BMT (AlloBMT) was performed in 500 patients and autologous BMT (ABMT) in 499 patients. For both groups, an abnormal chromosome (abn) 5 and/or 7 or a hypodiploid karyotype had a poor outcome, whereas t(15;17), pseudodiploidy, hyperdiploidy and diploidy were associated with a standard prognosis. Abn (16) and t(8;21) were also of standard prognosis for ABMT, but favorable for AlloBMT. When comparing AlloBMT and ABMT in patients with favorable or standard cytogenetics, AlloBMT was of benefit for remission duration and leukemia-free survival (LFS). Patients with an unfavorable karyotype had a similar outcome, regardless of type of BMT. By multivariate analysis, cytogenetics at diagnosis had the strongest prognostic value for relapse, LFS, and survival in AlloBMT. In ABMT, cytogenetics influenced relapse and LFS. We concluded that the karyotype at diagnosis had important prognostic implication in AML grafted in CR1.