In this uni-centre retrospective study, we studied 120 adults with acute myeloid leukaemia (AML) (n = 88) and myelodysplastic syndrome (MDS) (n = 32) who received first allogeneic HSCT to determine prognostic factors which are correlated with the outcome after myeloablative (MA) or non-myeloablative (non-MA) allogeneic HSCT. The median age of our cohort was 44 years. Fifty-nine per cent of the patients were transplanted in complete remission (CR) and 41% were in relapse or refractory to induction or salvage therapy. A total of 97 patients received a MA regimen and 23 were treated with a non-MA regimen. The prognostic impact for several parameters was assessed by univariate and by multivariate analyses using the Cox regression model. Three-year probabilities of non-relapse mortality (34 vs. 54%; p = 0.9) did not differ in the MA and non-MA groups, but differences were observed in the disease-free survival (DFS) (43 vs. 17%; p = 0.1) and the relapse rate (RR) (29 vs. 62%; p = 0.01). Independently from the regimen, in uni- and multivariate analysis, survival was best in those patients who were transplanted in CR and experienced cGvHD. Interestingly, outcome of patients with complex cytogenetic aberrations was identical to that of better prognostic subgroups. In this study, the clinical benefit of a lower toxicity regimen was offset by higher RR resulting in inferior results in the non-MA group, especially when no CR was achieved by prior induction or salvage therapy.