Pharmaceuticals are one of the most used compounds present in various environmental compartments. Due to their high consumption and possible unhealthy effect on ecosystems, pharmaceuticals have been identified as “emerging organic contaminants”. Since these compounds have medium to high polarity, they end up in the water compartment after being used. This work deals with the sorption of three pharmaceutical substances from the therapeutic group of antibiotics. Specifically we have focused on Azithromycin, Clarithromycin and Erythromycin. Three fractions of the natural Slovak zeolites (200 μm, 0.5—1 mm and 1.5—2 mm) were used as the sorption medium. Experimental results have proven very effective sorption of antibiotics by zeolites. Azithromycin removal of over 99 % for all three zeolite fractions from wastewater treatment plant Stupava and wastewater treatment plant Devínska Nová Ves was achieved. Clarithromycin removal of 79 % for fraction 1—2.5 mm, 87.3 % for fraction 0.5—1 mm and of 99.8 % for fraction 200 μm from the effluent of wastewater treatment plant Stupava was observed. Erythromycin removal of 31.3 % for fraction 1—2.5 mm, 66.9 % for fraction 0.5—1mm and of 94.7 % for fraction 200 μm from effluent of wastewater treatment plant Stupava was measured. More than 95 % of Clarithromycin and Erythromycin were eliminated from the effluent of wastewater treatment plant Devínska Nová Ves. The highest elimination percentage was observed for the smallest zeolite fraction due to the highest specific surface area.