Abstract We studied Major Histocompatibility Complex (MHC) Class I and Class II genes in seven Mexican Mestizo patients with Takayasu arteritis. Takayasu arteritis is an uncommon condition in Mexican Mestizo, however, previous studies report association of the disease in this population with Human Leukocyte Antigen (HLA)-B39 and HLA-DRB1*1301. The results in the present study show that the haplotypes of the Mexican Mestizo patients with Takayasu arteritis are very heterogeneous, even when the disease is much more rare in Mexico than in Japan. The sequence analysis of HLA-B39 shows that Mexican patients exhibit the HLA-B*39061 and HLA-B*39062 subtypes. These subtypes are more common in Mexico than in Japan, where the predominant subtype is HLA-B*3901. Interestingly, HLA-B*39061 and B-39062 share the 3′ end of intron 2 and the 5′ end of exon 3 with HLA-B*5101 and B*52012, alleles associated to Takayasu arteritis in Japanese. This fact suggests that Takayasu arteritis patients may share a specific sequence rather than a specific allele, even when the gene involved in the susceptibility to develop Takayasu arteritis may be a neighboring gene located between the genes related at present time with the disease, i.e. a gene located between MHC Class I and Class II regions.