Background: Although most adults are infected by Epstein-Barr virus (EBV), some patients develop highly lethal diseases associated with EBV infection, including EBV-hemophagocytic lymphohistiocytosis (EBV-HLH), chronic active EBV infections (CAEBV), and lymphoma, the pathogeneses of which remain to be investigated. The human leukocyte antigen (HLA) complex may be associated with the viral infection pathway, and, therefore, HLA alleles may be associated with EBV-related diseases and subpopulations of infected cells, studies related to EBV-associated diseases, and subpopulations of infected cells that were conducted in China are scarce. Methods: In this study, we analyzed the high-resolution HLA genotypes of 269 patients with EBV-associated diseases and 213 EBV-seronegative hematopoietic stem cell donors using PCR-SBT assay and elucidated the associations of HLA-A, -B, -C, -DRB1, and -DQB1 alleles with EBV-associated diseases in the Chinese population, Benjamini-Hochberg correction to adjust for multiple testing. HLA genotypes were also analyzed in patients with EBV-associated diseases showing EBV-infected lymphocyte subpopulations. Results: We found that individuals carrying the following alleles showed the following levels of risks: HLA-DRB1*11 allele, reduced risk of EBV-related disease (OR [odds ratio]: 0.56; 95% confidence interval [95% CI]: 0.32-0.99; p < .05; Adjust p = .71); HLA-DQB1*06:02 allele, reduced risk (OR: 0.5699; 95% CI: 0.3486-0.9317; p < .05; Adjust p = .57); and HLA-B*15:01 allele, increased risk (OR: 1.763; 95% CI: 0.3486-0.9317; p < .05; Adjust p = .57). Patients with EBV-associated diseases showing the B*15:01 genotype had a higher risk of T-cell, NK-cell, and multicell infections than those with other genotype subgroups. Conclusions: These findings highlight the importance of HLA genotype for assessing EBV infectivity.