The composite system can be prepared by incorporation of methylene blue into the channels of zeolite and by adsorption on the surface of the crystals. The composite photosensitizer effectively absorbs the red light (λmax = 648 nm) and upon illumination with light-emitting diode at a fluence rate of 1.02 mW cm-2 generates effectively reactive singlet oxygen in aqueous solution, which was proved by EPR spectroscopy. To test efficiency for inactivation of pathogenic microorganisms we measured photokilling of bacteria Escherichia coli and Staphylococcus aureus and yeasts Candida albicans. We found out that after the microorganisms have been adsorbed at the surface of such modified zeolite, the photogenerated singlet oxygen quickly penetrates their cell walls, bringing about their effective photoinactivation. The growth inhibition reached almost 50 % at 200 and 400 mg modified zeolite in 1 ml of medium in Escherichia coli and Candida albicans, respectively. On the other hand, the growth inhibition of Staphylococcus aureus reached 50 % at far smaller amount of photocatalyst (30 µg per 1 ml of medium). These results demonstrate differences in sensitivities of bacteria and yeast growth. The comparison revealed that concentration required for IC50 was in case of Candida albicans several orders of magnitude lower for a zeolite-immobilized dye than it was for a freely dissolved dye. In Staphylococcus aureus this concentration was even lower by four orders of magnitude. Thus our work suggested a new possibility to exploitation of zeolite and methylene blue in the protection of biologically contaminated environment, and in photodynamic therapy.