Peroxynitrite is a cytotoxic intermediate produced by the reaction between a superoxide anion radical and nitric oxide. The scavenging activities of flavonoids on peroxynitrite were investigated to illustrate the structure-activity relationship. Peroxynitrite was scavenged by the presence of various flavonoids, whose structures seem to be closely related to the degree of scavenging. Of 31 compounds tested, the most active was quercetin, with an IC50 value of 0.93 microM. Others had IC50 values ranging from 0.96 to more than 10 microM. The scavenging activity was postulated to be governed by the position of the hydroxyl group. Ortho-hydroxyl structures increased the scavenging activity on peroxynitrite.