Flavonoids represent one of the oldest, largest, and most diverse families of plant secondary metabolites. These compounds serve a wide range of functions in plants, from pigmentation and UV protection to the regulation of hormone transport. Flavonoids also have interesting pharmacological activities in animals that are increasingly being characterized in terms of effects on specific proteins or other macromolecules. Although flavonoids are found in many different locations both inside and outside the cell, biosynthesis has long been believed to take place exclusively in the cytoplasm. Recent reports from a number of different plant species have documented the presence of flavonoids in nuclei, raising the possibility of novel mechanisms of action for these compounds. Here we present evidence that not only flavonoids, but also at least two of the biosynthetic enzymes, are located in the nucleus in several cell types in Arabidopsis. This is the first indication that differential targeting of the biosynthetic machinery may be used to regulate the deposition of plant secondary products at diverse sites of action within the cell.Flavonoids represent a major class of plant secondary metabolites that include the flavonols, anthocyanins, proanthocyanidins (condensed tannins), and isoflavonoids. These compounds are well known for their roles in flower pigmentation, UV protection, signaling, male fertility, and defense against microbial pathogens (1-3). Flavonoids are also of significant interest as antioxidant and anticancer agents in the human diet (4 -7), and nutritional engineering is being used to modify the types and amounts of flavonoids produced by vegetable crops such as tomato and soybean (8 -10).Flavonoids are synthesized via a well-characterized biosynthetic pathway that has been localized to the cytoplasm in many different plant species (11-13). The products are then deposited in a variety of cellular locations. In some tissues, such as the epidermis of leaves and flowers and endothelium of the developing seed coat, flavonoids are transported primarily to the vacuole by processes that appear to involve multidrug resistance-associated protein or multidrug and toxic compound extrusion proteins (14 -16). In other tissues, a significant proportion of flavonoids are deposited in the cell wall (17)(18)(19)(20) or secreted (21-23). Vesicles apparently involved in transport of flavonoids to the cell periphery have been described in sorghum plants responding to fungal infection (24) and in maize cells induced to accumulate anthocyanins (25). This localization may occur via alternative secretory pathways not involving the Golgi (26). Flavonoids that regulate basipetal auxin transport in the root may also be moved across the cell in some manner because flavonoid enzymes have been localized to the opposite end of the cell from the auxin transport proteins, with which flavonoids are proposed to interact (27). A large proportion of flavonoids can even remain in the cytoplasm in some tissues; for example, interaction of fla...