The increasing need for the provision of high-quality and healthy animal food products, coupled with the occurrence of infectious diseases in livestock, such as avian influenca and swine fever, has meant that society at large has become increasingly aware of issues associated with the quality of food products of animal origin, as well as animal breeding, animal health and animal welfare. They illustrate the interaction between the social and economic significance of high-quality food production on the one hand and animal welfare and animal health on the other. With the establishment of the research programme “FUGATO – Functional Genome Analysis in Animal Organisms” in 2004, the German Federal Ministry of Education and Research (BMBF) recognised the high value-added potential of innovative solutions for problems associated with livestock breeding. Within the scope of FUGATO, competent research networks in academia and industry are deciphering the molecular mechanisms associated with important traits in productive livestock. Important insights, required for the production of high-quality animal food products by optimising livestock breeding, will be gained as a result. FUGATO aims to focus national expertise and build networks in the areas of animal breeding, veterinary medicine and bioinformatics. Focusing efforts in this manner has helped to profile national animal breeding research on a European level. A bilateral cooperation with France has already been initialised.