Metabolomics, which is defined as the comprehensive analysis of metabolites in a biological specimen, is an emerging technology that holds promise to inform the practice of precision medicine. Historically, small numbers of metabolites have been used to diagnose complex metabolic diseases as well as monogenic disorders such as inborn errors of metabolism. Current metabolomic technologies go well beyond the scope of standard clinical chemistry techniques and are capable of precise analyses of hundreds to thousands of metabolites. Consequently, metabolomics affords detailed characterization of metabolic phenotypes and can enable precision medicine at a number of levels, including the characterization of metabolic derangements that underlie disease, discovery of new therapeutic targets, and discovery of biomarkers that may be used to either diagnose disease or monitor activity of therapeutics.