Flavonoids, present in fruits, vegetables, and teas, provide beneficial effects for our health. We investigated the effect of a number of flavonoids on tight junction (TJ) barrier integrity in human intestinal Caco-2 cells. Transepithelial electrical resistance (TER; a TJ integrity marker) across cell monolayers was measured in cells incubated with flavonoids for 24 h. Chrysin decreased the TER, indicating a decrease in TJ integrity. Daidzein, hesperetin, naringenin, and morin increased the TER, indicating increased TJ integrity. Luteolin and genistein increased or normalized the TER after a transient decrease. Immunoblot analysis revealed that these changes in TER were caused by modification of the cytoskeletal association and expression of TJ proteins, zonula occludens (ZO)-1, ZO-2, occludin, junctional adhesion molecule-1, and/or claudins. Our results suggest that various flavonoids participate in the regulation of intestinal TJ barrier integrity and that this regulation may partially contribute to the flavonoid-mediated biological effects on our health.