Optimal therapy for patients with acute myeloid leukemia (AML) in first complete remission (CR-1) remains the subject of debate: with the possibilities of chemotherapy alone, autologous (auto) or allogeneic (allo) hematopoietic stem cell transplantation (HSCT). We undertook a retrospective analysis of AML patients aged below 46 years and in CR-1, who had undergone auto- or allo-HSCT in our institution, to determine the factors associated with a better outcome. Between September 1985 and April 2003, 81 patients underwent autologous (n = 29) or allogeneic (n = 52) HSCT in CR-1. With a median follow-up of 10 years, the probability of 15-year overall survival (OS) was 51%[95% confidence interval (CI) = 32 - 70%] for auto-HSCT vs. 55% (95% CI = 42 - 69) for allo-HSCT, respectively (P = 0.92). The cumulative incidence of relapse at 3 years was 49% (95% CI = 30 - 67) (auto) vs. 21% (95% CI = 10 - 30) (allo), respectively. Non-relapse-related mortality at 3 years was 5% (95% CI = 0 - 14) (auto) vs. 17% (95% CI = 7 - 28) (allo), respectively. This retrospective analysis confirmed that auto- and allo-HSCT led to similar OS. The significantly lower incidence of relapse amongst allograft recipients was balanced by an increased incidence of death in CR.