The aim of this study was to evaluate extramedullary (EM) relapses and its features in an allogeneic hematopoietic stem cell transplantation (alloHSCT) cohort, which consisted of patients with acute leukemia and advanced-phase chronic myeloid leukemia. One hundred and twenty-eight alloHSCT patients transplanted between the years 2001 and 2014 were analyzed. EM relapses observed in acute lymphoblastic leukemia (ALL) were more frequent than that of in acute myeloid leukemia (AML) and CML, although calculation of cumulative risk incidence, BM relapse, EM relapse, and non-relapse mortality were considered as competing risks of each other. At the 60th month, estimated CBMR and CEMR incidences were, respectively, 14.3 (5.1)% and 25.9 (6.6)% in ALL, 25.8 (5.9)% and 15.5 (4.8)% in AML, and 61.5 (16.5)% and 17.9 (13.4)% in CML. Among multiple parameters, the only type of conditioning regimen (p:0.046), EM involvement at diagnosis (p:0.009), and the presence of GVHD were found to be associated with EM relapse risk independently (p: 0.045). Chronic GVHD and TBI-based regimens significantly decreased the EM relapse risk, whereas it was higher with Mel/Flu and its variants. In conclusion, EM relapse is not uncommon after alloHSCT. GVHD and TBI-based regimens may prevent this complication.