Research object: a phenomenon of genetic structure changes of the red dairy cattle populations under the influence of selection on the productivity increase. Research objective: to evaluate the effectiveness of Immunogenetic markers in selection of the red dairy cattle. Research methods: Immunogenetic, population and genetic, biometric. Theoretical and practical results: there have been developed and improved methods of analysis, profound evaluation and selection of highly effective genotypes in the dairy cattle populations on the basis of molecular and genetic markers. Sphere of use: dairy cattle breeding.