Flavonoids are a diverse group of phenolic secondary metabolites that occur naturally in plants and therefore form an integral component of the human diet. Many of the compounds belonging to this group are potent antioxidants in vitro and epidemiological studies suggest a direct correlation between high flavonoid intake and decreased risk of cardiovascular disease, cancer and other age-related diseases. Modifying flavonoid biosynthesis in chosen crops may provide new raw materials that have the potential to be used in foods designed for specific benefits to human health. We report that flavonoid biosynthesis in tomato fruit is subject to tissue specific and developmental regulation. Using transgenic modification, we have investigated the role of several of the enzymatic steps of tomato flavonol biosynthesis. Furthermore, we have generated several tomato lines with significantly altered flavonoid content. Most notably achieving an up to 78-fold increase in total fruit flavonols through ectopic expression of the biosynthetic enzyme, chalcone isomerase. This increase results principally from the accumulation of quercetin-glycosides in peel tissue. In addition, we report that chalcone synthase and flavonol synthase transgenes act synergistically to significantly up-regulate flavonol biosynthesis in tomato flesh tissues. A review of this work is presented in this paper.