The human can be thought of as a human-microbe hybrid, and the health of this superorganism will be affected by intrinsic properties such as human genetics, diurnal cycles, and age and by extrinsic factors such as lifestyle choices (food and drink, drug intake) and the acquisition of a stable "healthy" gut microflora (the so-called microbiome). Alterations in this superorganism will be manifest in the metabolite complement within its serum and urine samples. The unraveling of this metabolic compartmentalization in this complex ecosystem will certainly be a challenge for systems biology and necessary for defining human health at the molecular level. Within the systems biology framework, functional analyses at the level of gene expression (transcriptomics), protein translation (proteomics), and, more recently, the metabolite network (metabolomics) have become increasingly popular. Metabolomics experiments aim to quantify all metabolites in a cellular system (cell or tissue) under defined states and at different time points so that the dynamics of any biotic, abiotic, or genetic perturbation can be accurately assessed. This article provides an overview of metabolomics and discusses how data are generated and analyzed within a systems biology framework. The role of metabolomics in nutrigenomics is also discussed, as are the concepts of the human being a superorganism and the complexities required to be overcome to understand human health and disease.