Metabolomics approaches enable the parallel assessment of the levels of a broad range of metabolites and have been documented to have great value in both phenotyping and diagnostic analyses in plants. These tools have recently been turned to evaluation of the natural variance apparent in metabolite composition. Here, we describe exciting progress made in the identification of the genetic determinants of plant chemical composition, focussing on the application of metabolomics strategies and their integration with other high-throughput technologies. Metabolomics represents an important addition to the tools currently employed in genomics-assisted selection for crop improvement.