The purpose of this study was to develop an in vitro permeation model that will predict the fraction of drugs absorbed in humans. A rotating-diffusion cell with two aqueous compartments, separated by a lipid-impregnated artificial membrane, was used to determine the permeability of drugs under conditions of controlled hydrodynamics. The measured effective permeability coefficient was modified to include the paracellular transport derived from a previously reported colorectal adenocarcinoma epithelial cell line (Caco-2) permeability study and the effects of unstirred water layer anticipated in vivo. Permeability data were collected for 31 different marketed drugs with known absolute oral bioavailability and human hepatic clearance data. Literature bioavailability values were corrected for the first pass hepatic clearance thus obtaining the fraction absorbed from intestinal lumen (fraction absorbed), F a, while assuming that the fraction escaping intestinal extraction, F g, was approximately ∼1. Permeability obtained under conditions of controlled hydrodynamics was compared with the permeability measured under unstirred conditions. It is shown that the optimized effective permeability correlates with the fraction absorbed. In contrast, permeability data obtained under unstirred conditions does not show a good correlation. The in vitro permeation model developed in this study predicts the fraction absorbed of the selected drugs in humans within experimental uncertainty. It has been demonstrated that the correlation with the fraction absorbed is greatly improved using the permeability data obtained under controlled hydrodynamics with paracellular transport included in the model. © 2011 Elsevier B.V. All rights reserved.