Good health is attributed to a combination of genetics, lifestyle, and diet. Evidence for healthy foods requires novel strategies able to predict personalised responses to the food we eat. Because metabolomics allows the analysis of physiological processes through the monitoring of metabolite concentration, it is suited to measure the metabolic effects of diet. This chapter covers the use of biomarkers in nutrition and applications of state-of-the-art metabolomics technologies to understand nutritional effects on metabolism. Special emphasis is given to the metabolic interaction between host and gut microbiota, a key player in the digestion and biotransformation of metabolites from dietary sources. © 2013 Woodhead Publishing Limited All rights reserved.