Sixty-four patients with Takayasu's arteritis and 156 healthy individuals in the Japanese population were examined for HLA-B specificity at the DNA level by DNA typing using polymerase chain reaction (PCR)/sequence-specific oligonucleotide probe (SSOP) analysis and by subsequent sequencing analysis. The frequency of epitope combination group-B52 (EC-B52) corresponding precisely to HLA-B52 specificity and that of EC-B39.2 which is a newly-identified subtype of HLA-B39 specificity were increased in the patient group. These two disease-associated HLA-B alleles share an epitope composed of 63Glu and 67Ser. Because two HLA-B alleles, HLA-B51 and B39.1, which are similar but different at the epitope from HLA-B52 and B39.2, respectively, are not associated with Takayasu arteritis, 63Glu and 67Ser are supposed to be involved in the pathogenesis.