To elucidate the associations of the HLA class II alleles with Graves' disease (GD), we examined DRB1, DQA1, DQB1 alleles in 62 Japanese GD patients and 142 control subjects by the PCR-SSOP (polymerase chain reaction-sequence specific oligonucleotide probes) method. We found that DRB1*0803 (P<0.02), DRB1*1403 (P<0.03), DQA1*0103 (P<0.02) alleles and DRB1*0803-DQA1*0103-DQB1*0601 (P<0.01), DRB1*1403-DQA1*0501-DQB1*0301 (P<0.02) haplotypes were significantly increased in GD patients. No DQB1 allele revealed a significant association with GD in Japanese. These weak associations may reflect either the heterogeneity of GD in Japanese or the importance of non-HLA factors in the development of the disease.