Disease susceptibility is in part controlled by human genome diversity. We and others have investigated the association between the susceptibility to various vasculitis of unknown etiology and HLA. For example, aortitis syndrome (Takayasu disease) is associated with HLA-B＊5201, IKBLp*03, and DRB1*1502, while thromboarteritis obliterans (Buerger disease) is associated with HLA-DRB1*1501 and DPB1*0501. In addition, recent analysis has revealed that chronic thromboembolic pulmonary hypertension without prior deep venous thrombosis is also associated with HLAB*5201, IKBLp*03, and DPB1*0202, while no association with HLA alleles was observed for chronic thromboembolic pulmonary hypertension with prior deep venous thrombosis. In this review, I will summarize the findings of HLA association with vasculitis and discuss about the role of human genome diversity in the pathogenesis, by focusing on the genes in the HLA region.