Trans-racial analysis of disease association has improved mapping of MHC-linked susceptibility to insulin dependent diabetes mellitus (IDDM). In this study, the contribution of the HLA class II DQA1 and DQB1 genes was investigated. Nine DQA1 and 10 DQB1 sequence-specific oligonucleotide gene probing in 49 IDDM and 48 control subjects from Beijing showed that DQA1-A4 alleles was positively associated with the disease (RR = 11.7, Pc < 0.02) as was the Asp57 negative homozygotes of DQB1 gene (P < 0.01, RR = 5.3), and that Asp57 positive homozygote of DQB1 gene conferred protection against IDDM (P < 0.025, RR = 0.38). Compared with trans-racial study, the decrease of Asp57 negative homozygote frequence and increase of Asp57 positive homozygote frequence in Chinese population may contribute to the low incidence of IDDM.