A high sensitivity reversed-phase HPLC method is presented for the simultaneous determination of marker compounds of paracellular transport (atenolol), transcellular transport (propranolol) and P-gp functionality (talinolol) in the Caco-2 system. The Caco-2 system is presently commonly accepted as an in vitro cell culture model of the intestinal mucosa. A programmed wavelength fluorescence detection method was used to optimise the response of the marker compounds. This marker compound mixture and the corresponding HPLC assay can be used for in house validation of the Caco-2 system or to evaluate simultaneously the effect of test compounds or absorption enhancing strategies on monolayer integrity and P-gp functionality. The method can easily be adapted to determine the concentration of atenolol, propranolol and talinolol in blood, thus allowing to use the same compounds in the in situ rat perfusion system with blood sampling from the mesenteric vein.