In the context of increased globalisation and competitiveness, producers of animal products have been the most affected with considerable reductions in profit margins. Research on nutrition in farm animals is thus still needed to reduce the costs of production by increasing metabolic efficiency. To achieve this goal, the objective is always to control animal performance accurately by improved quantification of animal requirements and by precise feed evaluation. At the same time, the farming and agri-food sectors are faced with a general saturation of food markets in Europe and with an increasing demand by consumers for high-quality meat and dairy products. This has also led to specific research in nutrition which aims to optimise metabolic activity of muscle and mammary gland to produce meat and dairy products of the desirable composition. This paper aims to address this important question: how animal nutrition may help to optimise metabolic efficiency and product quality. Today this needs better knowledge of tissue and organ requirements and of nutrient fate within tissues and organs as well as of their contribution to the quality of animal products. Furthermore, in order to achieve this goal of greater understanding of animal response to nutrition, new concepts and techniques are available to decipher mechanisms that were impossible to address adequately a few years ago. In this connection, emerging approaches such as genomics and modelling provide the means for a better insight into the mechanisms which regulate metabolism at tissue or whole body level.