It has been established that the absorption of many drugs from the small intestine is hindered by the detoxification systems which are present in this epithelial tissue. In this article, we will summarize the significant role of small intestine in reducing the oral bioavailability of drugs, particularly focusing on the role of metabolic enzymes and efflux transporters. Since the role of cytochrome P450 3A (CYP3A) and MDR1 P-glycoprotein (P-gp) in intestinal drug disposition has been highlighted, the disposition of CYP3A substrates, P-gp substrates and CYP3A/P-gp bisubstrates are summarized. Moreover, it is plausible that conjugative enzymes and/or carboxyesterases act synergistically with efflux transporters of organic anions, affecting the intestinal availability, i.e. many xenobiotics and ester-type prodrugs are metabolized to the corresponding glucuronide and sulfate conjugates and carboxylates (active drugs), respectively, followed by cellular extrusion. The characteristics of the efflux transporters of organic anions across the apical and basal membrane of enterocytes and Caco-2 cells are also summarized from this point of view.