To analyze the prognostic factors of extramedullary relapse (EMR) after allogeneic hematopoietic stem cell transplantation (allo-HSCT) in acute lymphoblastic leukemia (ALL).The clinical data of 33 relapsed patients in 95 ALL patients receiving allo-HSCT were analyzed retrospectively. The median time of relapse was 5.7 (0.7-52.3) months. Extramedullary relapse was recorded in 10 cases (10.5%), bone marrow relapse in 15 cases (15.8%), and both extramedullary and marrow relapse were seen in 8 cases (8.4%). The median time of EMR was 7.4(0.7-52.3) months. The most commonly involved organ was central nervous system, followed by testis and bone. The 3-year OS rate in EMR patients was (33.3±11.1) %. Univariate analysis showed that disease state before transplantation ( P=0.026), extramedullary infiltration before transplantation ( P=0.005), conditioning regimens ( P=0.033) and acute graft-versus-host disease(aGVHD) ( P=0.013) were significantly correlated with EMR. Multivariate analysis suggested that extramedullary infiltration ( RR=5.067, 95 %CI1.542-16.645, P=0.007) and aGVHD( RR=3.585, 95 %CI1.245-10.320, P=0.018) were independent predictive factors of EMR in ALL patients after allo-HSCT.