A brief review of quantum chemical studies of different active sites in zeolites is presented. Various factors that significantly affect the strength of Bronsted acid sites in zeolites are discussed. An interaction of zeolite protons with entrapped metal particles is considered as a reason of electron-deficiency of metal clusters in zeolite cavities on the Pd and Pt species as an example. Probable precursors of Lewis acid sites (LAS) and reliable molecular models of the LAS in zeolites are discussed on the basis of quantum chemical analysis. Transition metal ions can be catalytically active in the lattice or extra-lattice zeolite positions and the two possibilities are considered for selective oxidation site in titanium silicalite and FeZSM-5 zeolite catalysts, respectively.