Background: The association of human leukocyte antigen (HLA) alleles and Takayasu arteritis (TA) is not fully understood. The aim of the present study was to investigate HLA alleles in Japanese patients with TA and the association of these alleles with clinical manifestations. Methods and Results: A total of 96 patients diagnosed with TA according to the Guideline for Management of Vasculitis Syndrome (Japanese Circulation Society 2008) and 371 healthy controls were enrolled in the present study. HLA genotyping showed a significant association of HLA-B67 (P=0.00024, odds ratio [OR]=4.94), a novel locus, and B52 (P<0.0001; OR=3.35), a conventional locus, with TA using both sequence-based typing and PCR-SSP assay. The frequency of HLA-B39, an allele reportedly associated with TA in Asian populations, was not higher than controls in the present study (P=0.86, OR=1.07). B52 had higher prevalence than B67 but the OR was higher for B67. We next studied the association of HLA-B67 and -B52 with clinical characteristics: age at disease onset, distribution of arteritis, pulmonary involvement, aortic regurgitation, systemic hypertension, steroid resistance and recurrence rate in TA. There was no significant difference in these clinical parameters between HLA-B67-positive or HLA-B52-positive patients and other patients. Conclusions: The HLA-B67 allele could be a new and important marker of TA because of its high OR compared to HLA-B52, although its prevalence in TA is lower.  (Circ J 2012; 76: 1697–1702)