The intrinsic clearance of an organ is usually approximated by the apparent clearance from that organ in the development of a physiologically based pharmacokinetic model. In this study, the exact relationship between the two clearances was derived and analyzed. When the extraction ratio of the drug was small (less than 0.05), the approximation was reasonable. However, when the extraction ratio was high (greater than 0.2), serious errors could be made by using the approximation. These errors could be as much as 50% reduction in the estimated extraction ratio and as much as an order-of-magnitude difference in the intrinsic clearance.