The process of polar auxin transport, central to a plant's auxin relations, can be inhibited by a group of synthetic compounds that apparently act by binding to a plasma membrane protein known as the naphthylphthalamic acid (NPA) receptor. No endogenous ligand to the NPA receptor, capable of affecting polar auxin transport in plants, has yet been found. It is now shown that a group of flavonoids-including quercetin, apigenin, and kaempferol-can specifically compete with [(3)H]NPA for binding to its receptor and can perturb auxin transport in a variety of plant tissues and transport systems in a manner closely paralleling the action of synthetic transport inhibitors. Because the active flavonoids are widely distributed in the plant kingdom and exert their effects at micromolar concentrations approximating likely endogenous levels, they may act as natural auxin transport regulators in plants.