Metabolomics is the study of metabolites present in biological samples such as biofluids, tissue/cellular extracts and culture media. Combining metabolomic data with multivariate data analysis tools allows us to study alterations in metabolic pathways following different perturbations. Examples of perturbations can be disease state, drug or nutritional interventions with successful applications in the fields of drug toxicology, biomarker development and nutrition research. Application of metabolomics to nutrition research is increasing and applications range from assessing novel biomarkers of dietary intake to application of metabolomics in intervention studies. The present review highlights the use of metabolomics in nutrition research.