HLA-DQA1 and -DQB1 genes were investigated in 30 Japanese children with idiopathic nephrotic syndrome (INS) using the polymerase chain reaction-restriction fragment length polymorphism method. Compared with control children, there was a significant increase in the HLA-DQA1*0501, DQB1*0301 and DQB1*0601 alleles, whereas the frequency of DQB1*0501 showed a significant decrease in the patients. The increase of DQA1*0501 can be explained as being a result of a linkage disequilibrium with DQB1*0301. The previous result demonstrating a positive association of DRw6 and DRw8 with INS is also assumed to be attributable to a linkage disequilibrium with DQB1*0301 and 0601. A total of 83% of patients compared with 37% of controls possessed DQB1*0301 and/or DQB1*0601 allele (P < 0.001, RR = 8.6). Only these alleles have alanine at residue 13 and tyrosine at residue 26 in the hypervariable region in the Beta 1 domain of DQB1 gene. These findings suggest that the unique amino acid residues in the DQB1 gene may contribute to disease susceptibility in Japanese children with INS.