Studies suggest a variety of biological effects for isoflavones and anthocyanins, but there is little information regarding small intestinal absorption and metabolism. In this article, absorption and metabolism studies of selected phytochemicals, especially isoflavones and anthocyanins are reviewed. To assess small intestinal absorption an isolated preparation of luminally and vascularly perfused rat small intestine was used, with a synthetic perfusate free from blood components as vascular medium. Luminal media consisted of a buffered sodium chloride solution spiked with the phytochemicals. Viability and functional integrity of the organ preparation was maintained during the entire perfusion. Venous and luminal aliquots were analyzed for the phytochemicals with HPLC. Complex foods (tofu) were predigested with an in vitro digestion system using pepsin and pancreatin before perfusion experiments. Vascular uptake of the lipophilic isoflavone genistein was higher than for the more hydrophilic glycosides genistin, daidzin and cyanidin-3-glucoside. The isoflavone glycosides were hydrolyzed to their aglycons, which appeared at the vascular and luminal side. In contrast, anthocyanidin glucosides were not cleaved during perfusion experiments. All of the investigated phytochemicals were partly glucuronidated. These conjugates were vascularly absorbed and luminally secreted. Tofu ingredients influenced isoflavone uptake, extent of glucuronic conjugation and distribution of glucuronides in the small intestine. Ethanol, in contrast, had no significant influence on cyanidin-3-glucoside absorption. The investigated phytochemicals are absorbed at various extent in the small intestine, partly as conjugates. The implication of a simulated digestion and the use of the isolated perfused rat small intestine are suitable tools to investigate and evaluate the influence of food matrix on the intestinal handling of phytochemicals.