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Plant natural products have been used since ancient times as medicines and herbal remedies. Over the past two decades, the results of population and intervention studies, or assays in animal or cell model systems, have revealed positive health beneficial effects for various classes of phytochemicals, particularly polyphenols. The results of such studies have ignited an interest in being able to manipulate the levels of such bioactive compounds in plants using biotechnological approaches. Although still in its infancy, this technology promises to deliver health benefits to humans and animals through direct consumption of genetically-modified or -enhanced dietary plant materials. We here review the strategies currently being used for engineering two classes of nutraceuticals, the proanthocyanidins and the isoflavones, in transgenic plants. We also provide an overview of recent advances in our understanding of the biosynthesis of these classes of compounds.