Aim Allele DNA typing has significantly increased the level of diversity revealing multiple functional variants. Some alleles are found in multiple populations with distinctive haplotype associations, suggesting convergent evolution. HLA has been under strong selection, owing to its fundamental role in the immune response. We analyzed alleles and three loci haplotypes distribution in Mexicans, because of the need to know thoroughly the HLA structure to look into disease associations and BMT donors selection. Methods A total of 87 healthy Mexicans registered at DONORMO-The Mexican Unrelated Bone Marrow Donor Registry , born in different states of Mexico were included. DNA samples were sequenced in an ABI Prism 310. The Allele and Haplotype (HF) analysis was performed with the Arlequin 3.5.1.2 software using the maximum likelihood method. Results The 10 most prevalent A∗-B∗-DRB1∗ haplotypes (HF =0.052-0.017) were ∗02:06-∗39:05-∗04:07, Hispanic; ∗02:01-∗35:12-∗08:02, Mexican Natives, Mestizos & , Hispanic ; ∗02:06 -∗14:02-∗01:02, rare ; ∗02:01-∗52:01 ∗15:02 European ; ∗11:01-∗18:01-∗ 11:04, Mediterranean ; ∗24:02-∗52:01-∗14:06, rare; ∗26:01-∗44:02 -∗04:02 Hispanic; ∗33:01-∗14:02-∗01:02 Mediterranean; ∗33:01-∗78:01-∗13:02, rare ; & ∗68:03-∗39:05 -∗04:07 Mexican, Hispanic . Conclusions Even some alleles are found in many different populations, they are grouped with distinctive haplotypic associations, suggesting distinct genetic events may have occurred. Unique or rare A∗-B∗-DRB1∗ haplotypes are present such as: ∗ 02:06- ∗ 14:02- ∗ 01:02, HF=0.029%; ∗ 24:02- ∗ 52:01- ∗ 14:06, HF=0.017%, ∗ 33:01- ∗ 78:01- ∗ 13:02 HF= 0.017% . The first is rarely found in Europe. The second one is unique to Hispanics (0.00025) and the last one is rare only in Africans (0.00065). We found 12 more haplotypes not ever detected in any other population and three more with HF=0.011. The relevance of these data in transplantation are undoubtful. The process of donor selection will be directed more efficiently for patients with these genetic profiles.