Plant secondary metabolism is highly regulated within the major pathways to terpenoids, phenolics and alkaloids. Such regulation can occur at multiple levels from transcription through to the compartmentation of the product. However, the possibility exists for cross-talk between these pathways, the regulation of which is largely unknown at present. Such phenomena are important to understand in the application of plant breeding, where unintended effects of transgenesis or mutation can have an impact on the environment or human health. In an effort to improve dietary antioxidant content of crop plants, the tomato has been a major focus of effort for engineering both lipophilic antioxidants such as carotenoids and hydrophilic antioxidants such as flavonoid glycosides. In this study, a panel of transgenic and mutant tomato lines has been subjected to metabolite profiling in comparison with wild type Ailsa Craig for both carotenoids and phenolics. A range of mutants and transgenic lines were selected showing a range of phenotypes varying from down-regulation through to increased levels of lycopene and beta-carotene. All mutants altered in structural genes for carotenoid biosynthesis showed that perturbations in carotenoid biosynthesis do not generally alter phenolic or flavonoids content significantly even when devoid of carotenoids. Reciprocally, the down-regulation of ferulate 5-hydroxylase had no effect on carotenoid content. In contrast mutants defective in light perception such as the high pigment (hp-1) and LA3771 possess elevated chlorogenic acid and rutin as well as increased carotenoid content. These lines can act as the hosts for further genetic manipulation for increased antioxidant content.