Insufficient knowledge on absorption, distribution, metabolism and excretion limits drug discovery. Chemical synthesis of molecules and testing in experimental animals preceeds human use of drug candidates. However, this approach has low throughput and significantly decreases speed of drug finding. Therefore, in order to predict behavior of novel structures prior to the first administration in humans molecular descriptors are employed. Molecular descriptors can be applied in modeling relevant properties of molecules such as passive transcellular permeability, solubility, unspecific binding to proteins or volume of distribution. In addition, sets of molecular descriptors can be used to predict interaction of a molecule with biological membranes or proteins. They can also be used to predict regions around the molecule relevant for efficacy. Molecular descriptors have successfully been applied in many problem solving approaches in drug discovery and the future use of them is expanding.