Animal diseases cause significant losses to livestock’s and breeders, resultant into direct damages to animals, reduced productivity and cost of treatment. One of the promising additional methods to control diseases is breeding animals for disease resistance. The resistance of animals to diseases is related to their ability to withstand pathogens and harmful environmental influences. For the planned control of hereditary diseases in domestic animals, it is required not only an accurate knowledge of their inheritance but also an accurate and monotonous description and designation of the disease. Therefore, in order to avoid misunderstandings in identifying hereditary anomalies in domestic animals, an international nomenclature has been created for their description and designation. According to this nomenclature, hereditary diseases of each species of animals are designated by a certain letter of the alphabet. Specific diseases peculiar to this species are characterized by numerical indexes. Developments in technologies, such as genomic selection, may help overcome several of the limitations of traditional breeding programmes and will be especially beneficial in breeding for lowly heritable disease traits that only manifest themselves following exposure to pathogens or environmental stressors in adulthood. The current paper provides a brief overview of the present-day application of microsatellites markers in animal breeding and makes a significant contribution to the overall farm animal health and resistance to disease.