Oral bioavailability of pharmacologically effective drugs is often limited by first-pass biotransformation. In humans, both hepatic and intestinal enzymes can catalyze the metabolism of a drug as it transits between the gastrointestinal lumen and systemic blood for the first time. Although a spectrum of drug biotransformations can occur during first-pass, the most common are oxidations catalyzed by cytochromes P450. It is the isozymes CYP2D6, CYP3A4, CYP1A2, CYP2C9 and CYP2C19 that are most often implicated in first-pass drug elimination. For any given substrate, enzyme specificity, enzyme content, substrate binding affinity and sensitivity to irreversible catalytic events all play a role in determining the overall efficiency, or intrinsic clearance, of elimination. Several models have been proposed over the past twenty-five years that mathematically describe the process of drug extraction across the liver. The most widely used, the well-stirred model, has also been considered for depiction of first-pass drug elimination across the intestinal wall. With these models it has been possible to examine sources of interindividual variability in drug bioavailability including, variable constitutive enzyme expression (both genetic and environmentally determined), enzyme induction by drugs, disease and diet, and intrinsic or acquired differences in plasma protein binding and organ blood flow (food and drug effects). In recent years, the most common application of hepatic clearance models has been the determination of maximum organ availability of a drug from in vitro derived estimates of intrinsic metabolic clearance. The relative success of the in vitro-in vivo approach for both low and highly extracted drugs has led to a broader use by the drug industry for a priori predictions as part of the drug selection process. A considerable degree of effort has also been focused on gut wall first-pass metabolism. Important pathways of intestinal Phase II first-pass metabolism include the sulfation of terbutaline and isoproterenol and glucuronidation of morphine and labetalol. It is also clear that some of the substrates for CYP3A4 (e.g., cyclosporine, midazolam, nifedipine, verapamil and saquinavir) undergo significant metabolic extraction by the gut wall. For example, the first-pass extraction of midazolam by the intestinal mucosa appears, on average, to be comparable to extraction by the liver. However, many other CYP3A substrates do not appear susceptible to a gut wall first-pass, possibly because of enzyme saturation during first-pass or a limited intrinsic metabolic clearance. Both direct biochemical and indirect in vivo clearance data suggest significant inter-individual variability in gut wall CYP3A-dependent metabolism. The source of this constitutive variability is largely unknown. Because of their unique anatomical location, enzymes of the gut wall may represent an important and highly sensitive site of metabolically-based interactions for orally administered drugs. Again, interindividual variability may make it impossible to predict the likelihood of an interaction in any given patient. Hopefully, though, newer models for studying human gut wall metabolic extraction will provide the means to predict the average extraction ratio and maximum first-pass availability of a putative substrate, or the range of possible inhibitory or inductive changes for a putative inhibitor/inducer.