We studied HLA class I (HLA-A, -B) and class II (HLA-DRB1, -DQB1) alleles by PCR-SSP based typing in 88 Mexicans from the state of Querétaro living in the city of Querétaro (N = 45) and rural communities (N = 43), to obtain information regarding allelic and haplotypic frequencies. We find that the most frequent haplotypes in the state of Querétaro include seven Native American, two European and one Asian haplotype. Admixture estimates revealed that the main genetic components in the state of Querétaro are Native American (51.82 ± 4.42% by ML; 42.61% of Native American haplotypes) and European (48.18 ± 3.55% by ML; 46.02% of European haplotypes), with a virtually absent African genetic component (0.00 ± 4.25% by ML; 4.55% of African haplotypes). Copyright © 2019 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.