The development of nutrigenomic studies has brought about a number of new research tools (transcriptomics, proteomics and metabolomics), which are important in animal nutrition and food research. This review presents an overview on the application of nutrigenomics tools in this scientific area. The use of microarray technologies - the main tools of transcriptomics, has allowed new information concerning the physiological effect of different dietary proteins, of omega-3 polyunsaturated fatty acids and dietary conditioning of colon cancer, to be obtained. The use of proteomics tools (mainly two-dimensional electrophoresis) revealed new information concerning the protein composition of egg and poultry meat proteins, the effect of dietary methionine on breast-meat accretion, the toxicity of dioxin and the safe use of transgenic crops in animal nutrition. Metabolomic analysis allowed the detection of changes in the biochemical profiles of plasma and urine from pigs fed different diets and the determination of metabolite profiles in the liver of rats used as an animal model to characterize the toxicity of triazol fungicides. In livestock species, the microarray technology was discussed and reviewed as potential nutrigenomics tools, in context to its economic benefi ts and improvement of the food quality and safety in dairy and meat industries. However, the newly emerged nutrigenomics tools like - gene expression-based biomarker development still poses a major challenge. Finally, latest developments in the standardization of metobolomics data in relation to functional genomics, nutrigenomics and toxicology studies are discussed.