The aim of this study was to compare the efficacy of lamivudine vs entecavir in the prevention of hepatitis B virus (HBV) reactivation in HBV surface Ag (HBsAg)-positive patients undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT). A total of 216 consecutive patients were enrolled and retrospectively reviewed. Of these patients, 119 received lamivudine and 97 received entecavir. The median treatment duration to complete virological response in patients with baseline HBV-DNA levels 410 5 copies/mL was 2.0 months in the entecavir group, significantly shorter than that of the lamivudine group. After a median follow-up of 24 months post transplantation, the cumulative incidence rates of HBV reactivation at 6, 12 and 24 months following transplantation were 3.0%, 7.0% and 24.0% in the lamivudine group, and 0%, 0% and 2.0% in the entecavir group, respectively. In addition, entecavir treatment was associated with lower cumulative incidence rates of severe hepatitis caused by HBV reactivation. Mutations leading to drug resistance were detected in 25 patients in the lamivudine group and in only one patient in the entecavir group. Our data indicate that compared with lamivudine, entecavir has more potent antiviral efficacy and may be a better choice for prophylaxis of HBV reactivation in HBsAg-positive allo-HSCT recipients.