To investigate the effect of elevated CO2 and O3 on the accumulation of flavonoids in Ginkgo Biloba leaves, four-year-old trees were exposed in open-top chambers with ambient and twice ambient CO2 and O3 concentrations singly and in combination in 2006. The results show that elevated CO2 reduce the concentrations of keampferol aglycon (-10%), isorhamnetin aglycon (-15%). Elevated O3 reduce the concentrations of the isorhamnetin aglycon (-7%), but increase the concentration of quercetin aglycon (+6%). Under elevated CO2 and O3 in combination, O3-derived effects on flavonoids concentrations are changed by elevated CO2, which are similar to that under the elevated CO2 alone. In conclusion, the concentrations of flavonoids are influenced by the changes in leaf dry mass induced by elevated CO2 and elevated O3. Furthermore, some flavonoids may not respond as antioxidant under ozone stress in ginkgo leaves.