Identification of the primary allele(s) in HLA class II associated diseases remains challenging because of a tight linkage between alleles of HLA-DR and -DQ loci. In the present study, we determined the genotypes of seven HLA loci (HLA-A, -B, -DRB1, -DQA1, -DQB1, -DPA1 and -DPB1) for 1200 Japanese patients with primary biliary cholangitis and 1196 controls. Observation of recombination derivatives facilitated an evaluation of the effects of individual HLA alleles consisting of disease-prone/disease-resistant HLA haplotypes. Consequently, a primary contribution of DQB1* 06:04 (odds ratio:0.19, p = 1.91 x 10(-22)), DQB1* 03:01 (odds ratio:0.50, p = 6.76 x 10(-10)), DRB1* 08:03 (odds ratio:1.75, p = 1.01 x 10(-7)) and DQB1* 04:01 (odds ratio:1.50, p = 9.20 x 10(-6)) was suggested. Epistasis of the protective DQB1* 06:04 to risk conferred by DRB1* 08:03 was demonstrated by subpopulation analysis, implicating the presence of an active immunological mechanism that alleviates pathogenic autoimmune reactions. Further, the contribution of the aforementioned HLA alleles as well as an HLA-DP allele, DPB1* 02:01 to the association signals of 304 loci among 4103 SNPs in the HLA region at the genome-wide level of significance (p values less than 5 x 10(-8)) was demonstrated by the stepwise exclusion of the individuals possessing these HLA alleles from the comparison.