"Omics" technologies provide coverage of gene, protein and metabolite analysis that is unsurpassed compared with traditional targeted approaches. There are a growing number of examples indicating that profiling approaches can be used to expose significant sources of variation in the composition of crop and model plants caused by genetic background, breeding method, growing environment (site, season), genotype × environment interactions and crop cultural practices to name but a few. Whilst breeders have long been aware of such variation from tried and tested targeted analytical approaches, the broad-scale, so called "unbiased" analysis of the metabolome now possible, offers a major upside to our understanding of the true extent of variation in a plethora of metabolites relevant to human and animal health and nutrition. Metabolomics is helping to provide targets for plant breeding by linking gene expression, and allelic variation to variation in metabolite complement (functional genomics), and is also being deployed to better assess the potential impacts of climate change and reduced input agricultural systems on crop composition. This review will provide examples of the factors driving variation in the metabolomes of crop species.