To investigate the distributions of HLA-A*02 alleles in Han populations and compare their difference between the south and north in China.A total of 208 individuals from south China and 109 from north China were randomly selected from registered bone marrow donors in Chinese Han population, who were tested positive for HLA-A*02 alleles by PCR with sequence-specific primers (PCR-SSP). Genotyping of the alleles was performed using PCR-sequence-based typing (PCR-SBT).Six different HLA-A*02 alleles (A*020101, A*0203, A*0205, A*0206, A*0207 and A*0210) were identified in the two Chinese Han populations, of which A*0207(37%) was the predominant allele in southerners and A*020101(48%) in the northerners. A*020101(31%), A*0203(16%) and A*0206(14%) were common alleles in the southerners in comparison with A*0206(21%) and A*0207(23%) alleles in the northerners. The overall distribution of A*02 alleles and the frequencies of A*020101, A*0203 and A*0207 in the two populations differed significantly. The heterozygosity of A*02 in the southerners and northerners was higher than 90% and 80% at the high- and low-resolution levels, respectively, and the distribution of A*02 homozygote at low-resolution level in both populations showed diversity and regularity at high-resolution level.HLA-A*02 alleles possess high heterogeneity and genetic diversity in Chinese Han population with significantly different distributions in the two populations. HLA-A**020101, A*0203 and A*0207 may serve as the genetic markers for dividing Chinese Han individuals into southerners and northerners in anthropological studies.