These authors contributed equally to this work Purpose: To evaluate the role of Decitabine in the allo-HSCT conditioning regimen for intermediate-and high-risk patients with MDS or AML. Patients and methods: Retrospective analysis of data pertaining to 76 intermediate-and high-risk patients with MDS or AML who underwent allo-HSCT between December 2005 and June 2018 at the Peking University First Hospital. Forty patients received Decitabinecontaining conditioning regimen before transplantation, while thirty-six patients received regimen without Decitabine.Results: Over a median follow-up of 40 months (range, 1 to 155), the cumulative incidence of grade II to IV acute graft versus host disease was 12.4% [95% confidence interval (CI) 4.9-30.9%] in the Decitabine group and 41.5% (95% CI 28.1-61.2%) in the non-Decitabine group (P=0.005). On multivariate analysis, Decitabine-containing conditioning regimen was found to protect against grade II to IV aGVHD (HR=0.279, 95% CI 0.102-0.765, P=0.013). Incidence of respiratory infection in the Decitabine and non-Decitabine groups was 22.5% and 52.78%, respectively (P=0.012). No significant between-group difference was observed with respect to 3-year OS, DFS, or RR (P=0.980, 0.959, and 0.573, respectively), while the median relapse time was longer in the Decitabine group [7 months (range, 2-12) versus 3 months (range, 2-4), P=0.171]. Decitabine-containing conditioning showed a tendency for lower relapse rate among higher risk patients, as assessed by IPSS R; however, the betweengroup difference was not statistically significant (P=0.085). Conclusion: Inclusion of Decitabine in the conditioning regimen for allo-HSCT in intermediate-and high-risk patients may lower the incidence of aGVHD and respiratory infections, and contribute to longer median relapse time.