The purpose of this study was to continue our effort to determine how enzyme-transporter coupling affect disposition of flavonoids. The rat intestinal perfusion and Caco-2 cell models were used together with relevant microsomes. In perfusion model, isoflavone (i.e., formononetin and biochanin A) absorption and subsequent excretion of its metabolites were always site-dependent. Maximal amounts of intestinal and biliary conjugates excreted per 30 min were 31 and 51 nmol for formononetin, more than that for pure biochanin A (12 and 20 nmol). When a standardized red clover extract (biochanin A/formononetin ϭ 10:7) was used, the results indicated that more metabolites of biochanin A than formononetin were found in the perfusate (36.9 versus 22.8 nmol) and bile (78 versus 51 nmol). In metabolism studies, rat intestinal and liver microsomes always glucuronidated biochanin A faster (p Ͻ 0.05) than formononetin, whereas intestinal microsomes glucuronidated both isoflavones faster (p Ͻ 0.05) than liver microsomes. However, rapid metabolism in the microsomes did not translate into more efficient excretion in either the rat perfusion model as shown previously or in the Caco-2 model. In the Caco-2 model, both isoflavones were rapidly absorbed, efficiently conjugated, and the conjugates excreted apically and basolaterally. More formononetin conjugates were excreted than biochanin A when used alone, but much more biochanin A conjugates were found when using the isoflavone mixture. In conclusion, efficiency of enzyme-transporter coupling controls the amounts of metabolites excreted by the intestine and liver and determines the relative contribution of enteric and enterohepatic recycling to the in vivo disposition of isoflavones.Red clover (Trifolium pratense L.) extracts are sold as dietary supplements in supermarkets and health food stores in both industrialized and developing countries. Several defined extracts of red clover are sold in the United States to treat women who suffer from menopausal-related symptoms (Rijke et al., 2001;Oleszek and Stochmal, 2002). The extracts are available as tablets (e.g., Promensil), capsules, tea, liquid preparations, and several other forms. Limited clinical studies have demonstrated the effectiveness of Promensil in the management of hot flashes (van de Weijer and Barentsen, 2002), although the efficacy of such products is not always consistent (Baber et al., 1999;St. Germain et al., 2001).Red clover extract contains many of the same isoflavones as soy (Lin et al., 2000). However, a majority of isoflavones in red clover are present in aglycone forms, whereas they are present as glucosides in soy and soy extracts. Furthermore, the principal isoflavones are biochanin A and formononetin in red clover but are genistein and daidzein in soy. Nevertheless, these isoflavones all have similar biological activities, and biochanin A and formononetin can be converted to genistein and daidzein by cytochrome P450 (Tolleson et al., 2002;Hu et al., 2003b). Moreover, daidzein can be metabolized to h...