Inborn errors of metabolism are characterized by dysregulation of the metabolic networks that underlie development and homeostasis, and constitute an important and expanding group of genetic disorders in humans. Diagnostic methods that are based on molecular genetic tools have a limited ability to correlate phenotypes with subtle changes in metabolic fluxes. We argue that the direct and dynamic measurement of metabolite flux will facilitate the integration of environmental, genetic and biochemical factors with phenotypic information. Ultimately, this integration will lead to new diagnostic and therapeutic approaches that are focused on the manipulation of these pathways.