Allo-SCT with reduced-intensity conditioning (RIC) results in lower non-relapse mortality (NRM), but higher relapse rate than myeloablative conditioning (MAC) in AML/myelodysplastic syndromes (MDS). Novel regimens with intensive anti-leukemic activity, but with limited toxicity will be of benefit. In all, 85 patients with AML/MDS, not eligible for MAC, were given fludarabine-treosulfan conditioning (FT). Outcomes were compared with those in patients given fludarabine-BU RIC (FB2, n=106) or reduced-toxicity (RTC) conditioning (FB4, fludarabine and myeloablative BU dose, n=85). The 5-year NRM was 29%, 20% and 18% after FT, FB2 and FB4, respectively (P=NS). Multivariate analysis (MVA) identified comorbidity score (HCT-CI) >2 and advanced disease as adverse factors with no independent impact of regimen. The 5-year relapse rate was 36%, 47% and 40%, respectively (P=0.17). MVA identified advanced disease as the major adverse factor, while FT had significantly lower relapse rate (hazard ratio 0.6, P=0.03). The 5-year survival (OS) was 37% with advanced disease. HCT-CI >2 and age ≥ 50 were found as adverse factors. The 5-year OS was 46%, 44% and 50% after FT, FB2 and FB4 in early-intermediate-stage disease (P=NS) and 33%, 9% and 28% in advanced disease, respectively (P=0.02). FT is an RTC regimen with intensive anti-leukemia effect in MAC non-eligible patients.