We identified human leukocyte alloantigens (HLA) class II alleles in 24 Japanese children with steroid-sensitive nephrotic syndrome (SSNS) by deoxyribonucleic acid (DNA) typing. The DQA1 and DQB1 alleles were identified using sequence-specific oligonucleotide probes for DQA and DQB. The frequency of DQB1*0302 was significantly higher in the patients than in the controls (54.0 vs. 16.0%, respectively; relative risk, RR = 6.2; pc < 0.00009. We also found that the frequency of DQA1*0103 in the patients was significantly lower than in the controls (RR = 0.194, pc < 0.04). Several studies have identified an association between certain HLA by serotyping. In the present study, we investigated the HLAs of Japanese patients with SSNS by DNA typing and observed a significant increase in the frequency of DQB1*0302 in patients with the disease. HLA-DQ3, which was proven to be associated with SSNS, consists of HLA DQ7, 8 and 9. DQB1*0302 is a component of HLA-DQ8. So we proposed the increase of DQ3 was due to an increase in DQ8.