The major histocompatibility complex genes (mhc) encode MHC I and II molecules which present peptide fragments to T cells. Therefore these polymorphic molecules critically influence susceptibility to infectious diseases. At present study potential relationship between amino acid sequences in the antigen binding groove of different BoLA-DRB3 alleles and susceptibility or resistance to calf diarrhea was investigated. Twelve different DRB3 alleles were found among 171 calves (84 diarrheic and 87 healthy) analyesd by PCR-RFLP method. Amino acid sequences of the encoded peptide binding region were compared. 26 polymorphic positions were detected in this region. A significant association (p< 0.05) was shown between occurrence of diarrhea and the presence of glutamic acid and tyrosine in pocket 4 and valine, glutamine and leucine in pocket 9 of peptide binding region. Thus it can be concluded that pockets 4 and 9 of the BoLA-DRB3 molecule would be involved in conferring susceptibility of calf to diarrhea.