Objective To explore the association of HLA-B allele polymorphism with type 2 diabetes mellitus (T2DM) in Han ethnicity of Jiangsu region. Methods One hundred and eighteen patients with clinically diagnosed T2DM were examined. HLA-B typing was performed using polymerase chain reaction with sequence-based genotyping (PCR-SBT). The frequency of HLA-B alleles and serotypes in the group with T2DM was compared with that in Han ethnic healthy populations (644 persons and 20248 persons) from Jiangsu branch of Chinese National Marrow Donor Program (CMDP). Results Compared with the healthy donors, there was an increased frequency of HLA-B *1501 (8.90% vs 3.03%, Pc =0.000, ■ = 3.13, 95% CI = 1.80-5.42, statistical power = 98.23%) and a decreased frequency of HLA-B *5801 (1.69% vs 8.62%, Pc = 0.000, ■ = 0.18, 95% CI = 0.07-0.50, statistical power = 91.07%) in the group with T2DM. Accordingly, a higher frequency of HLA-B *15 serotype (21.18% vs 13.03%,Pc = 0.022, ■ = 1.79, 95% CI = 1.26-2.55, power = 90.15%) and a lower frequency of HLA-B*58serotype (1.69% vs. 8.62%, Pc = 0.000, ■ = 0.18, 95% CI = 0.07-0.50, power = 91.09%) were found in the T2DM group. Conclusions HLA-B*1501 allele may be a marker of susceptibility for T2DM, in reverse, HLA-B*5801 allele is possibly associated with a resistant effect on T2DM in Han ethnicity of Jiangsu region. These data suggest, for the first time, the association of HLA class I genes with the T2DM in Chinese population.