One major prerequisite for an orally administered drug is the ability to cross the intestinal epithelia from intestinal lumen into the blood circulation. Therefore, the absorption potential of molecules is studied early on during the drug development process. Permeation experiments using cultured cell monolayers are one of the most often applied methods to screen and also to predict in more detail the intestinal absorption potential of molecules in preclinical phase. Furthermore, these studies are also used to screen the molecules for transporter interactions as well as for more detailed mechanistic studies of the transfer routes involved. Several mathematical and computational models with complexity varying from simple non-mechanistic single barrier models to mechanistically more detailed compartmental models have been developed to describe the drug disposition during these in vitro permeation experiments. This MiniReview gives an overview of these models and their applications. Also the implications of these models to the prediction of intestinal absorption in vivo are discussed.