The decipherment of the human and yeast as well as numerous pathogen genomes has resulted in an explosion of DNA sequence data. Additionally, a plethora of expressed sequences from various tissues and cells are available that cover much more than the estimated actual number of genes within a eukaryotic genome. Although the homology between the mammalian chromosomes, genomes and genes is well conserved simplifying genome analysis in livestock, the latter may be considered as in statu nascendi when compared to the state of development in humans or the mouse. However, this situation is not a surprise, as it has never been the aim of genome analysis projects in livestock to sequence all economical important species completely. The development of genome analysis of the major livestock species also shows that there is not an exponential increase in data. This again, is in contrast to human genome analysis and has mainly two reasons. Firstly, genome analysis in livestock so far has focused on the molecular identification and characterization of major economical important traits (ETLs=economic trait loci, QTL=quantitative trait loci). As the majority of these traits presumably are regulated by a large number of genes, it is conceivable that up to now QTL mapping has only resulted in the isolation of very few traceable major genes. Secondly, there are not many disorders that are of general importance for animal breeding, e.g. stress susceptibility in swine caused by a point mutation in the skeletal muscle ryanodine receptor gene or bovine leukocyte adhesion deficiency caused by a point mutation in the CD18 gene. As a consequence, financial support by breeding organizations or industry is still limited and scientists find it often difficult to convince public funding authorities that genome analysis in livestock as well as the development and implementation of DNA-based diagnosis in breeding programs is not only for the improvement of livestock production but also a contribution to animal welfare. This review summarizes the current state of genome analysis in the major livestock and domestic species, i. e. cattle, pig, sheep, goat, horse and chicken. Special emphasis will be placed on the comparison of availability and development of high-resolution marker maps which facilitate QTL mapping and rapid gene localization. One of the long-term aims of genome analysis in livestock as well as other domestic animals is to obtain genetic screening tests that will improve the health and welfare by selective breeding. There is a great and justifiable optimism that the efforts in genome analysis in livestock will provide new opportunities to identify genes causative for a number of disorders and will improve our understanding of complex traits for the benefit of livestock, livestock production and last but not least the consumer.