Peroxynitrite (ONOOH/ONOO-) which is formed in vivo under oxidative stress is a strong oxidizing and nitrating agent. It has been reported that several flavonoids, including quercetin, inhibit the peroxynitrite-induced oxidation and/or nitration of several molecules tested; however, the mechanism of their protective action against peroxynitrite is not univocally resolved. The kinetics of the reaction of quercetin with peroxynitrite was studied by stopped-flow as well as by conventional spectrophotometry under acidic, neutral and alkaline pH. The obtained results show that the protective mechanism of quercetin against peroxynitrite toxicity cannot be explained by direct scavenging of peroxynitrite. We propose that quercetin acts via scavenging intermediate radical products of peroxynitrite decomposition (it is an excellent scavenger of ·NO2) and/or via reduction of target radicals formed in the reaction with peroxynitrite.