The 3' hydroxylation of kaempferol forms quercetin with an orthodihydroxy structure having two neighboring hydroxyl groups that could theoretically chelate with metal ions and mediate oxidative phenomena. Colorless flavonoids were purified by high pressure liquid chromatography (HPLC) and screened by diode array analysis. The accumulation of quercetin derivatives in Arabidopsis was coordinately regulated with flavonoid biosynthesis in a chalcone isomerase mutant having reduced flux through the biosynthetic pathway, but not within differing wild-type tissues, where seedling, floral, and leaf tissue have a reduced ratio of quercetin to kaempferol derivatives, respectively. The accumulation of lipid peroxidation products in kaempferol proficient mutant seedlings was indistinguishable from that in quercetin proficient wild-type seedlings, leaving no evidence for the role of quercetin antioxidants. However, laser scanning confocal microscopy revealed quercetin derivatives lining the tonoplast of diphenylboric acid 2-aminoethyl ester-stained Arabidopsis seedling tissue and floral papillae, and Norfluorazon induced oxidative stress decreased the most lipophilic of HPLC purified quercetin derivatives. Its potential involvement with lipophyllic oxidative phenomena may warrant further study.