Tomato has quickly become a favoured species for metabolomics research. Tomato fills a niche that cannot be occupied by Arabidopsis, particularly regarding studies on fleshy fruit. Variations in genotype and phenotype have been broadly exploited using metabolomics approaches in order to gain a better understanding of fundamental aspects of plant physiology, fruit growth and fruit development. The commercial importance of tomato as one of the world's most important and widely grown and consumed vegetables is a significant driving force behind this fruit research. Therefore, many metabolomics studies have specifically been focused on traits of importance to the food and agro-industries. Fruit quality, nutritional value as well as the influence on these traits of fruit storage, transport and processing into pasteurized and cooked products have also been subjects for extensive metabolomics analyses. These studies have already considerably expanded our knowledge, and continue to do so, concerning many aspects of the tomato fruit phenotype, both visible and chemical. Furthermore, increased knowledge of the genetics of tomato, the recently available draft of the tomato genome sequence as well as the emerging technologies for next generation sequencing, large-scale phenotyping and systems biology approaches have generated many novel research concepts that are also placing metabolomics analyses of tomatoes right at the forefront of fruit research.