Tomato fruit and its products are one of the most widely consumed fruits and vegetables in the world. They are important components of the human diet supplying essential micronutrients. In addition to being an important economic crop, tomato is also a model for all crop plants. Excellent genetic resources exist in tomato culminating in the recent release of the tomato genome sequence (www.solgenomics.net). The depth and breath of chemical diversity found in tomato has also contributed to the development of metabolomics/metabolite profiling expertise in tomato and other Solanaceae. In the present article the natural variation in tomato that exists in the form of the Solanum pennellii near isogenic introgression (Il) collection have been utilized and subjected to large-scale multi-platform metabolite analysis. This approach has created a valuable resource on the chemical composition of tomato that can complement the genome sequence now available. To date approximately two thousand molecular features for each of the 76 Ils over the tomato genome have been quantified and tentative assignment of metabolites performed. In order to validate the dataset several putative metabolites associated with important traits have been unambiguously identified and quantified using targeted procedures. For each Il genotype integration and correlation analysis on the data has been performed. Collectively the data generated has provided (i) a valuable metabolite resource, (ii) a rapid means of associating trait to metabolite and in some cases effecter gene and (iii) revealed valuable insights into the organisation of metabolism in tomato fruit and other plant systems.