Patients with therapy-related acute myeloid leukemia (t-AML) and myelodysplastic syndromes (t-MDS) have poor survival and high non-relapse mortality (NRM) after allogeneic stem cell transplantation. This retrospective study assessed the transplant outcomes of 29 consecutive patients with t-AML (83%) or t-MDS (17%) treated with allogeneic transplantation. The median age of patients was 51 years. Donors were mostly matched unrelated (52%), and 59% of patients received myeloablative conditioning. Two-year overall survival, event-free survival and relapse incidence were 37%, 34% and 33%; NRM was 17% at 100 days, and 32% at 2 years. Event-free survival was reduced in patients with high-risk cytogenetics (p = 0.02), Karnofsky performance status ≤ 80% (p = 0.001) and disease after induction ± consolidation (p = 0.006). NRM was higher in patients receiving > 2 therapy lines for previous cancer (p = 0.01) and in those allografted > 6 months from diagnosis (p = 0.03). In conclusion, allogeneic transplantation should be proposed timely to these patients after an accurate analysis of patient history.