Kappa casein (κ-CN) is milk protein that determines the size and specific function of the caseinmicelles, and its clevage by chymosine is responsible for milk coagulation. Any variation in genepromoter or coding sequence may change the expression of the gene or amino acid sequence,effecting functional properties of the protein. The mature κ-CN is encoded by part of the exon 3and the entire exon 4. Since exon 3 has 33 bp and exon 4 is 497 bp long, the major part of theprotein is encoded by exon 4. In this study we identified two SNPs in exon 1 and two in exon 4of the horse kappa casein gene (CSN3) and genotyped them in three horse breeds. The nucleotidesequence of the first exon was included in this study due to its possible role in the regulation ofthe CSN3 expression. Because these polymorphisms were analysed for the first time, we used areference method (RFLP) or at least two other complementig methods (Bi-PASA/PIRA andASA-PCR/PIRA), for molecular genetic analysis of above mentioned SNPs. The highestvariation in genotype frequencies was present in Slovenian cold blood breed. SNPs in exon 4cause amino acid (AA) change in the mature product, and may very well renderchemical/functional properties of the protein. Analysis of the consequences caused by changes inAA sequence, by online avaible program tools, comfirmed our hypotesis.