Extramedullary relapse (EMR) rarely occurs after allogeneic hematopoietic stem cell transplantation (HSCT) in leukemia. This study was to investigate the clinical characteristics of EMR.We retrospectively investigated 316 consecutive patients undergoing HSCT for acute leukemia or chronic myeloid leukemia (CML) at 2 institutions between January 2012 and February 2017. Furthermore, we analyzed and compared the risk factors and outcomes between EMR and bone marrow relapse (BMR).The 5-year cumulative incidence of EMR was 14.1%. The EMR incidence in acute myeloid leukemia, lymphoblastic leukemia, and CML was 17.5%, 18.9%, and 5.3%, respectively. CML had a lower EMR incidence rate. Compared to the BMR group, the EMR group had a longer median relapse-free time (10.5 months vs 5 months, P = .02), and the EMR group had a higher incidence rate of chronic graft-versus-host disease (50.0% vs 20.9%, P = .009). EMR had better estimated 3-year survival rates post-HSCT, and post-relapse, than did BMR (39.5% vs 9.5%, P < .001, and 21.9% vs 10.8%, P = .001). Multivariate analysis identified that adverse cytogenetics (hazard ratio [HR] = 9.034, P < .001) and extramedullary leukemia before HSCT (HR = 2.685, P = .027) were the independent risk factors for EMR after HSCT. In the EMR group, patients who achieved complete remission (CR) had a significantly better, estimated 3-year survival than did patients who did not achieve CR (38.4% vs 14.3%, P = .014).EMR is a significant contributor to mortality after HSCT, which appears to be resistant to most of the current therapies. Establishing effective strategies for EMR is important in improving outcomes after HSCT.