Jean Anthelme Brillat-Savarin coined the maxim ‘Dites-moi ce que vous mangez et je vais vous dire ce que vous eˆtes’ – ‘you are what you eat’ – in 1826.1 Almost a century later, scientists have access to the key analytical technologies, particularly metabolomics2 and bioinformatics,3 necessary to objectively characterise the effects of the tens of thousands of molecules present in foods, described by Baraba´si et al. as the dark matter of food,4 on human metabolism. Nutrimetabolomics accommodates strategies to study the diet–health relationships in the human body in which, ideally, all metabolites are analysed or quantified. The overall purpose of nutrimetabolomics can be split into three broad categories: (1) characterising the susceptibility of organisms varying in their health conditions as per their dietary intake, (2) understanding the effect of specific dietary compounds, foods or dietary patterns on human metabolism and (3) identifying and validating markers of dietary intake. This review presents an overview of the concepts and applications of metabolomics to nutritional research. The different study designs used in human nutrimetabolomics studies are presented in Section 16.2, followed by a description of the dietary systems tested (Section 16.3). Section 16.4 presents an overview of the application of nutrimetabolomics to address the effects of nutrition on a broad range of diseases as well as on the maintenance of health status. Section 16.5 highlights mechanistic nutrimetabolomics studies and Section 16.6 presents a major application of metabolomics, which is the identification and validation of markers of dietary intake. Finally, the metabolomics analytical technologies are discussed in Section 16.7.