A key scientific objective of nutrition research is to determine the role of diet in metabolic regulation and to improve health. There are many new opportunities and challenges for the nutrition research in post-genome era. Novel omics technologies and bioinformatics tools offer enormous potential to investigate the complex relationship between nutrition and metabolism. An overview of omics technologies in nutrition research is presented in this paper, which focuses on recent applications of nutritranscriptomics, nutriproteomics and nutrimetabolomics in nutrition research. The potential limitations and future prospects are also discussed. The combination of various omics technologies, systems biology, will greatly facilitate the discovery of new biomarkers associated with specific nutrients or other dietary factors. It can be expected that the future omics-based human nutrition research can provide personalized dietary recommendations for disease prevention.