Our recent study indicates that microsomal glucuronidation rates are not predictive of the cellular glucuronide excretion rates and whole cell systems are needed to accurately determine the metabolic rates. This study aims to determine the contribution of UGT isoforms responsible for the metabolism of flavonoids in intact Caco-2 cells and cell lysates using siRNA. The results showed that UGT1A6 activities (as measured by p-nitrophenol glucuronidation) and expression were typically decreased 60-80% by siRNA treatment. Using siRNA-mediated silencing, we also showed that in intact cells, siRNA treatment substantially decreased the rate of excretion of apigenin glucuronide at low and high concentrations (>35%, p < 0.05), although it only moderately decreased the rate of excretion of genistein glucuronide at a high concentration (29%). The results also indicated that well-expressed UGT isoforms in the Caco-2 cells, UGT1A1, UGT1A3, UGT1A6, and UGT2B7, were capable of metabolizing apigenin faster than genistein and that UGT1A6 silencing did not substantially increase the level of expression of genistein-metabolizing UGT isoforms. We also determined the contribution of UGT1A6 to the apigenin and genistein metabolisms as a function of concentration, and the results indicated that metabolism of apigenin and genistein was saturable and siRNA treatment greatly reduced the rate of metabolism of apigenin but not that of genistein. In conclusion, we show for the first time that siRNA can be used effectively to determine which UGT isoform contributes to the metabolism of its substrate in intact cells. The results also indicate that UGT1A6 is a major contributor to glucuronidation of apigenin but not genistein in intact Caco-2 cells and in cell lysates.