Flavonoids comprise the most common group of polyphenolic plant secondary metabolites. In plants, flavonoids play an important role in biological processes. Beside their function as pigments in flowers and fruits, to attract pollinators and seed dispersers, flavonoids are involved in UV-scavenging, fertility and disease resistance. Since they are present in a wide range of fruits and vegetables, flavonoids form an integral part of the human diet. Currently there is broad interest in the effects of dietary polyphenols on human health. In addition to the potent antioxidant activity of many of these compounds in vitro, an inverse correlation between the intake of certain polyphenols and the risk of cardiovascular disease, cancer and other age related diseases has been observed in epidemiological studies. The potential nutritional effects of these molecules make them an attractive target for genetic engineering strategies aimed at producing plants with increased nutritional value. This review describes the current knowledge of the molecular regulation of the flavonoid pathway and the state of the art with respect to metabolic engineering of this pathway in crop plants.