The research area of animal genomics is moving now from its sequencing era into an integrativefunctional genomics era. Thefast growing sequence information of animal genomes provides exiting opportunities for improving animal health traits by genomics-assisted breeding approaches. In addition, data from functional genomics studies offers deeper insight into the biological mechanisms that underlie animal health phenotypes. Understanding host-pathogen relationships, for example, promises to forward the integration of health genetics into breeding programmes and the development of new tools and strategies for the diagnosis, prognosis, treatment and prevention of infectious diseases. Similarly, increased knowledge on nutrient-gene interactions provides information on the effects of nutrients on biological processes. This knowledge may be used to redefine and optimize the nutritional needs of healthy animals. In this paper, prospects, challenges, and requirements of animal genomics research for improving animal health will be presented.