In this study, we investigated HLA class I and class II allele and haplotype frequencies in Emiratis and compared them to those of Asian, Mediterranean, and Sub-Saharan African populations. Methods: Two-hundred unrelated Emirati parents of patients selected for bone marrow transplantation were genotyped for HLA class I (A,B,C) and class II (DRB1,DQB1) genes using reverse sequence specific oligonucleotide bead-based multiplexing. HLA haplotypes were assigned with certainty by segregation (pedigree) analysis, and haplotype frequencies were obtained by direct counting. HLA class I and class II frequencies in Emiratis were compared to data from other populations using standard genetic distances (SGD), Neighbor-Joining (NJ) phylogenetic dendrograms, and correspondence analysis. Results: The studied HLA loci were in Hardy–Weinberg Equilibrium. We identified 17HLA-A, 28HLA-B, 14HLA-C, 13HLA-DRB1, and 5HLA-DQB1alleles, of whichHLA-A*02(22.2%), -B*51(19.5%), -C*07(20.0%), -DRB1*03(22.2%), and -DQB1*02(32.8%) were the most frequent allele lineages.DRB1*03~DQB1*02(21.2%),DRB1*16~DQB1*05 (17.3%),B*35~C*04(11.7%),B*08~DRB1*03(9.7%),A*02~B*51(7.5%), andA*26~C*07~B*08~DRB1*03~DQB1*02(4.2%) were the most frequent two- and five-locus HLA haplotypes. Correspondence analysis and dendrograms showed that Emiratis were clustered with the Arabian Peninsula populations (Saudis, Omanis and Kuwaitis), West Mediterranean populations (North Africans, Iberians) and Pakistanis, but were distant from East Mediterranean (Turks, Albanians, Greek), Levantine (Syrians, Palestinians, Lebanese), Iranian, Iraqi Kurdish, and Sub-Saharan populations. Conclusions: Emiratis were closely related to Arabian Peninsula populations, West Mediterranean populations and Pakistanis. However, the contribution of East Mediterranean, Levantine Arab, Iranian, and Sub-Saharan populations to the Emiratis’ gene pool appears to be minor.