Metabolomics is a systems biology discipline wherein abundances of endogenous metabolites from biological samples are identified and quantitatively measured across a large range of metabolites and/or a large number of samples. Since all developmental, physiological and 'response to the environment' phenotypes have at least one metabolic component phenotype, metabolomics offers the opportunity to mechanistically dissect how metabolic processes participate in determining these complex phenotypes. Plants produce an amazingly diverse array of primary and specialized metabolites (>200000 kingdom-wide), many of which are integral for our food, feed, fibre and fuel industries. Thus, applications of metabolomics in plant genetics and breeding efforts offer efficient and effective solutions to challenges in our agricultural systems. This review briefly describes new advances in the metabolomic platforms and analysis methods that have been developed for both targeted and non-targeted metabolite profiling in plants. Special sections describing the application of these technologies are then provided for several relevant topics, including advances in plant quantitative genetics research, improved prediction of hybrid crop performance, mitigation of losses due to environmental stress, development of metabolic biomarkers for economically important traits, establishment of substantial equivalence between transgenic and conventional germplasm and biofortification for nutritional enhancement of our food supply. Future applications of metabolomics, particularly as a component discipline of phenomics, are also discussed.