The distribution of HLA-DRB1, -DQA1 and -DQB1 alleles were analysed in 124 Graves' disease (GD) patients compared to 124 normal controls in order to identify the alleles/haplotypes associated with GD in Thai population. The DRB1*1602-DQA1*0102-DQB1*0502 haplotype was significantly increased in GD patients (P = 0.0209, OR = 2.55). DRB1*07-DQA1*0201-DQB1*0201 haplotype (P = 0.039, OR = 0.32) and HLA-DRB1*12-DQA1*0601-DQB1*0301 haplotype (P = 0.0025, OR = 0.28) were significantly decreased in GD patients. Interestingly, a protective DRB1*07 allele in Thai population lacks an arginine at position 74 similar to DRB1*0311 (a protective allele in Caucasians). A significant association of DRB1*1602-DQA1*0102-DQB1*0502 and HLA-DRB1*12-DQA1*0601-DQB1*0301 alleles and haplotypes with GD was recently reported in Korean but not in any Caucasian studies. Thus, DRB1*1602 allele and closely linked haplotype, DRB1*1602-DQA1*0102-DQB1*0502, might serve as a marker for genetic susceptibility to GD in Asian population.