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Application of metabolomics to nutrition research is rapidly growing. Currently, the main areas where metabolomics plays a role in nutrition research are (1) identification of dietary biomarkers (2) study of diet-related diseases and (3) examination of metabolic effects due to nutrition interventions. The present review focuses on the role metabolomics can play in the discovery of dietary biomarkers. Achieving accurate assessment of dietary intake is one of the main hurdles in nutrition research. Classical self-reporting methods have a number of well-documented limitations, and there is a pressing need for more objective measures. In this respect, there is growing interest in dietary biomarkers and metabolomic applications offer a unique method for the identification of new dietary biomarkers. In recent years, a number of putative biomarkers have been identified using metabolomic-based approaches; however, validation of the biomarkers is still lacking. Further work is needed to demonstrate the true ability of these biomarkers in nutrition research.