A wide range of variation in immunogenetic and biochemical markers was found in thoroughbred Brown Carpathian cattle. Comparative analysis of genetic structure of Brown Carpathian and Swiss cattle, as well as various hybrids of these two breeds, with respect to polymorphic biochemical systems, demonstrated that all hybrids having any gene admixture of the Brown Carpathian breed formed a single cluster in a dendrogram and were readily distinguishable from thoroughbred Swiss cattle. Originally, the Swiss breed participated in forming the gene pool of Brown Carpathian cattle. The selective advantage of some gene associations, which included the loci of the biochemical genetic systems studied, was suggested to be a specific characteristic of the Brown Carpathian breed. Genetic differentiation in the groups of hybrids bred in regions with different ecological conditions (high- and lowland) was revealed.