Xanthine oxidoreductase (XOR) is one of the major targets for urate-lowering drugs. Inhibition of XOR reduces uric acid production, resulting in anti-gout effects. Studies of XOR-inhibitor interactions have revealed factors important in binding to the enzyme. Many foods have been reported to have urate-lowering properties, and various plant origine flavonoids have been shown to inhibit XOR. However, the Ki values of these compounds are 104 times higher than those of febuxostat. The crystal structure of XOR bound to quercetin reveals a lack of hydrogen bonding between the nitrile group and the asparagine residue of the enzyme, which is essential for potent inhibitory activity. These findings are expected to contribute to the development of new XOR inhibitors using flavonoids as lead compounds.