AIM: To investigate uptake characteristics of quercetin, luteolin, apigenin, genistein, daidzein, luteolin-7-O-β-D-galactoside, lonicerin, baicalin and rutin in the Caco-2 cell culture model system, and the relationship between uptake and structures of flavonoids. METHOD: The uptake of nine flavonoids were determined at different medium pH and different concentrations. RESULTS: The uptake of 9 flavonoids were the best at acidity medium; and the uptake all linearly increased with the increasing of sample concentrations; In pH5.5 medium the uptake of the 5 flavone aglycone is: quercetinluteolingenisteinapigenindaidzein; The uptake of the 4 flavone glycoside is: luteolin-7-O-β-D-galactosidelonicerinbaicalinrutin. CONCLUSION: ①Acidic medium is propitious to uptake of 9 flavonoids in Caco-2 cell culture model. The effect of pH on the uptake of Quercetin was the greatest, while Apigenin, Genistein, Daidzein smaller.②The nine flavonoids in Caco-2 cell culture model are absorbed through passive diffusion. ③The numbers of -OH and the location of B-ring affect the uptake of aglycone; The number, type and location of sugar play an important role in uptake of glycoside. This study also shows that the uptake of aglycone is much higher than that of glycoside.