Objective To explore the relationship between the polymorphism of allele HLA-A*02 and the incidence of nasopharyngeal carcinoma (NPC) of Han patients in Xinjiang. Methods Polymerase chain reaction/sequence-specific primers (PCR-SSP) method was adopted to analyze HLA-A alleles of 63 Han patients with NPC in Xinjiang and 51 health Han volunteers. The differences of allele HLA-A*02 and its subtypes of two groups were compared. Results The frequency of allele HLAA*02 in NPC patients was 39.7% (51/126) and the frequency of allele HLA-A*02 in healthy people was 16.7% (17/102). The difference was statistically significant (P=0.002). Seven subtypes of allele HLA-A*02 were detected in NPC patients and 4 subtypes of allele HLA-A*02 were detected in healthy people. The difference was not statistically significant (P>0.05). The differences of constituent ratios of subtypes were not statistically significant (P>0.05). Conclusion The allele HLA-A*02 is relevant to the incidence of NPC of Han patients in Xinjiang. The distribution of subtypes of allele HLA-A*02 of NPC patients in Xinjiang have their own features.