Patients with Acute Myelogenous Leukemia have a better outcome if reaching molecular remission. We compared the outcome of 373 patients autografted and 335 patients allografted with a 10/10 compatible unrelated donor in first molecular remission. Patients were stratified using the ELN European Leukemia Net classification. ELN favorable group: (234 auto and 70 unrelated transplants). By univariate analysis, in the auto group, the Non Relapse Mortality (NRM) was lower (3.7% versus 19%; P < 10−4), Relapse Incidence (RI) higher (29% versus 17%, P < 10−4), Leukemia Free Survival (LFS) identical (67% versus 64%) and Overall Survival (OS) better than in the allogeneic group (83% versus 62%; P = .008). By multivariate analysis, autologous transplantation was associated with a lower NRM (HR: 4, P = .01) and a better OS (HR: 2.08, P = .04). ELN intermediate group 1: (87 autologous and 172 unrelated transplants). By univariate analysis, in the auto group, NRM was lower (2.5% versus 11.8%; P = .03), RI higher (59% versus 18%, P < 10−6), LFS lower (39% versus 70%; P < 10−6) and OS lower than in the unrelated donor group (61% versus 74%; P = .005). By multivariate analysis, unrelated donor was superior to autologous transplantation for LFS (HR: 0.36, P < 10−5) and OS (HR: 0.53, P = .01). ELN intermediate group 2: (52 autologous and 93 unrelated donors). The outcome was identical. We conclude that good risk patients get higher benefit from autologous transplantation. Intermediate risk 2 patients have the same outcome and Intermediate risk 1 patients get higher benefit from unrelated donor transplants.