This study was aimed to explore the potential association of HLA-E polymorphism with the incidence of cytomegalovirus (CMV) infection after HLA-matched hematopoietic stem cell transplantation, 119 HLA-genoidentical sibling pairs for HLA-E polymorphism were analyzed, HLA-E DNA was amplified by polymerase chain reaction (PCR), and the amplified DNA products was also sequenced directly after purification to confirm the genotype. The results showed that the homozygous HLA-E*0101/0101 accounted for 20.17%, the homozygous HLA-E*0103/0103 accounted for 27.73%; heterozygous HLA-E*0101/0103 accounted for 52.10%; in homozygous HLA-E*0101/0101 group, 15 cases were infected with CMV and the CMV infection rate was 62.50%; in homozygous HLA-E*0103/0103 group, 16 cases were infected with CMV and the CMV infection rate was 48.48%; in heterozygous HLA-E*0101/0103 group 20 cases were infected with CMV and the CMV infection rate was 32.25%. As compared with the homozygous HLA-E*0101/0101 group, the CMV infection rate in HLA-E*0103 group displays statistical significance (P = 0.0295). The CMV infection rate occurred higher and its significance is statistical (P = 0.0074). It is concluded that the HLA-E gene polymorphism is associated with CMV infection after HLA-genoidentical bone marrow transplantation.