To investigate genetic factors involved in the pathogenesis of Takayasu arteritis, patients in the Japanese population were examined for HLA-A, -B, and -C alleles by serological typing and for HLA-DR, DQ, and DP alleles by DNA typing using polymerase chain reaction (PCR)/sequence-specific oligonucleotide probe (SSOP) analysis. The frequencies of HLA-Bw52, DRB1*1502, DRB5*0102, DQA1*0103, DQB1*0601, and DPB1*0901 alleles were significantly increased and the frequencies of HLA-Bw54, DRB1*0405, DRB4*0101, DQA1*0301, and DQB1*0401 alleles were significantly decreased. Strong linkage disequilibria among the increased alleles and among the decreased alleles were evident in the Japanese population. Therefore, the haplotype of HLA-B252-DRB1*1502-DRB5*0102-DQA1*0103-DQB1++ +*0601-DPA1*02-DPB1*0901 may confer susceptibility to Takayasu arteritis while another haplotype of HLA-Bw54-DRB1*0405-DRB4*0101-DQA1*0301-DQB1++ +*0401 may confer resistance to the disease. These observations clearly indicate that HLA-linked gene(s) are involved in the development of Takayasu arteritis.