BACKGROUND: Chicken major histocompatibility complex region (MHC) is important in the productive traits, immune responses, resistance to infectious diseases and phylogenetic relationships. OBJECTIVES: This study was investigated for single nucleotide polymorphisms of MHC region related to the immune system in commercial broiler and layer chickens. METHODS: One hundred blood samples were taken from commercial broiler and layer chickens and genomic DNA was extracted by salting out method. The allelic polymorphisms were investigated in B-L, B-F and B-G loci using PCR-RFLP and MspI enzyme. RESULTS: For two commercial broiler and laying populations, in the 374 bp locus of B-L, only BB genotype was detected but in the 1048 bp locus of B-F, two genotypes of CG and GG were identified in broiler chickens. The C allele contained four bands of 515, 410, 75 and 47 bp, and the G allele with five bands of 410, 302, 213, 75 and 47 bp. In B-G (401 bp) locus, three genotypes of MM, MN and NN and two alleles of M with one band (401 bp) and N with two bands (350 and 51 bp) were identified. In total populations, the Shannon information index was calculated to be 0.45 and 0.73 in markers loci of B-F and B-G, and the fixation index values were -0.20 and 0.34, respectively. The highest observed heterozygosity index for B-F and B-G loci was 0.34 and 0.23, respectively. CONCLUSIONS: Considering the confirmation of the presence of polymorphism in two loci of the B-F (in commercial broiler population) and B-G (in commercial broiler and layer populations), these sites can be used as genetic marker in breeding programs to increase resistance to diseases.