The intrabreed and interbreed genetic diversity of Lithuanian cattle breeds - two native, namely Lithuanian Light Grey and Lithuanian White-Backed and two modern, namely Lithuanian Red and Lithuanian Black and White was investigated by determination of genetic markers: 4 milk protein systems, Alpha(s1)-casein, Kappa-casein, Beta-casein and Beta-lactoglobulin, which are comprised of 12 different milk protein types. According to results, the B type of Alpha(s1)-casein was found as predominant in all four studied breeds. The most common A and B types of Kappa-casein were found at high frequency in all investigated cattle breeds. All investigated Lithuanian dairy cattle breeds had high frequency of Beta-lactoglobulin whey protein B types, with the highest frequency in Lithuanian Red breed, and the lowest in Lithuanian Light Grey. After investigation the diversity of alleles and genotypes of milk proteins in Lithuanian dairy cattle breeds was determined that, Lithuanian Red breed was distinguished private C allele and BC genotype of Beta-lactoglobulin and CC genotype of Alpha(s1)-casein. The interbreed genetic diversity was estimated by a principal component analysis (PCA). The first principal component (PC) explains 63.39% and the second principal component (PC) explains 33.67% of the genetics diversity between the breeds. Principal component analysis, suggests the hypothesis that native Lithuanian White Backed and Lithuanian Light Grey breeds still have traits tracing to old native populations.