The polymorphisms of the PRNP gene influence the susceptibility to scrapie in goats. In this study, caprine PRNP gene was analysed in a total of 249 individuals from three main indigenous goat breeds of Turkey: Anatolian Black, Angora and Kilis. We focused on the Anatolian Black breed, which represents 97% of the goat population in Turkey and compared the data of samples originated from different geographical regions. Eight polymorphisms were determined, given rise to 12 haplotypes. Allele, genotype and haplotype frequencies of the polymorphisms at codons 142, 143, 146, 154, 171, 211, 222 and 240 were calculated. Alleles associated to resistance to scrapie were found to be relatively rare in all breeds. The resistance allele 222K was absent in Turkish breeds. Other resistance-associated alleles: 146D, 146S, 154H and 171R were observed with low frequencies. The results of this study, which cover the mainly bred indigenous goats in Turkey, present the distribution of PRNP polymorphisms. Very low frequencies of resistance-associated alleles show the susceptibility to scrapie. The resistance-associated alleles S and D of codon 146 might be accepted as candidate alleles, due to their relative higher frequencies observed in the present study. A breeding program aiming to increase particularly the frequency of 146S might be applied. Predictions about impacts of a long-term breeding programme based on low initial allele frequencies and regarding its possible adverse effects are warranted. Our results might be a database for future breeding programmes, which should be carefully designed with adequate levels of genetic resistance and acceptable timeframe.