We investigated the prognostic role of somatic mutations in allogeneichematopoieticcelltransplantation (HCT) for denovomyelodysplasticsyndrome (MDS). We performed targeted deep sequencing analysis of 26 genes on bone marrow samples obtained within 6 weeks before HCT from 202 patients with denovo MDS. Overall, 76% of patients carried one or more somatic mutations, and TP53mutation was present in 23 patients (11.4%). Overall survival (OS) at 5 years was 63.6%, cumulative incidence of relapse (CIR) was 18.6%, event-free survival (EFS) was 58.5%, and non-relapse mortality (NRM) was 22.9%. TP53mutation was an independent risk factor for lower OS (41% vs. 67%; P = 0.001), higher CIR (49% vs. 15%; P = 0.001), and lower EFS (38% vs. 61%; P = 0.005), but not for NRM (13% vs. 24%). N-RAS mutation was an independent risk factor for higher CIR (HR, 5.91; P = 0.008). TP53mutation did not have significant interactions with conditioning intensity or the occurrence of graft-versus-host disease with regard to post-transplant outcomes. In conclusion, TP53mutation was significantly associated with poor outcomes after HCT for patients with denovo MDS, mainly due to a higher incidence of disease relapse.