Bovine spongiform encephalopathy (BSE) of the cattle is the outstanding disease among other transmissible spongiform encephalopathy (TSEs). It can be transmitted from the cattle to a human and causes a new variant of the Creutzfeldt-Jakob disease (CJD). It is known that prion protein coding gene (PRNP) plays a major role in the TSE susceptibility or resistance in some species. Recent researches demonstrated that the insertion (in) and deletion (del) polymorphisms within promoter and intron 1 region of the PRNP related to BSE susceptibility in cattle. In contrast to cattle, BSE has never been reported in water buffalo; hence, PRNP polymorphisms may be an explanation for buffalo resistance to BSE. The aim of this study was to evaluate allele, genotype, and haplotype frequencies of the PRNP promoter and intron 1 insertion/deletion (indel) polymorphism in healthy Anatolian, Murrah, and Murrah x Anatolian crossbred buffaloes. According to our findings, there were no deletion alleles at two mentioned loci. All studied buffaloes were monomorphic and have carried in/in haplotypes which are considered as the most resistant genotype to BSE.