During the last 30 years, the cattle genome map has been expanded from 4 genes linked on chromosome X to over 22,000 genes identified in the cattle genome sequence assembly. This progress has been achieved due to numerous projects on linkage and physical mapping of the cattle genome driven by its agricultural and scientific significance. Indeed, the high-resolution mapping and functional analysis of the genome led to the discovery of major quantitative trait loci (QTL) regions and several quantitative trait nucleotides (QTNs), as well as some disease genes in the cow population. In addition, a comparison of the cattle genome to the genomes of other mammals has revealed its unique features gained during the speciation and adaptation. With the development of non-expensive sequencing techniques, the analysis of the cattle genome will shift towards the identification of differences between breeds or individuals within breeds that account for the unique features of each breed. This approach holds promise for the development of effective tools for the marker assistant selection and disease diagnostics in cattle.