The high-throughput ‘omics’ technologies and especially metabolomics can play a major role in advancing the field of personalized medicine and associated fields like nutrition science. Current nutrition research is not mechanism driven making it difficult to fully understand (or forecast) the effects of diet and nutritional interventions. The omics biotechnology platforms can offer a more complete understanding of the complexity of biological systems, which is important for developing personalized nutrition strategies. Unlike transcriptomics and proteomics, metabolomics data encode the genotype and the phenotype. In order to fully understand the effects of diet on overall health status, it is important to be able to define the phenotype and show how it is affected by dietary factors. To this end, the gut microflora composition will also have an impact on the overall phenotype of an individual especially with regards to how nutrients are absorbed and utilized in the body. Metabolomics is uniquely suited to not only provide phenotype-specific information, but also to monitor dynamic changes in nutritional phenotypes, including variations over time, and how interventions such as dietary supplements may return phenotypes back into a normal range. This article provides an introduction to the field of metabolomics and how it may impact nutrition research especially with regards to defining mechanisms of action of bioactive food components, the role of the gut microflora, and the impact of nutritional interventions such as vitamin supplementation. Additionally, the challenges that must be overcome in order to apply metabolomics to its full potential in personalized nutrition are discussed.