The paper describes the investigation of the effect of three different types of hydrophobic zeolites (ultrastable zeolite type Y, pentasyl type zeolite (ZSM-5), and ALPO-5 type zeolite) on the pervaporation properties of zeolite-filled polydimethylsiloxane membranes. The procedure of obtaining membranes of various thicknesses varying in zeolite content was mastered. The physicochemical properties of the utilized zeolites were investigated and determined. The effect of zeolite type and concentration, as well as the membrane thickness and pervaporation temperature on the membrane permeability and selectivity were investigated. The physicochemical properties of the zeolite used, primarily the degree of hydrophobicity, as well as the sorption capacity for ethanol, the specific pore volume, specific area and mean crystallite size of the zeolite, significantly influence the membrane’s pervaporation properties. An increase in the zeolite content results in an increase of both membrane permeability and selectivity, while an increase in the pervaporation temperature results in an increase of the permeability and a decrease of selectivity, as opposed to the effect of membrane thickness.