The paper deals with the subject of increasing the efficiency of air purification in ventilation systems in situations of unusual hazardous indoor air pollutants. It analyzes possible locations of additional filtering and sterilizing elements in the installation to eliminate their return to the rooms. The quantities of pollutants in particular parts of the system were determined for a given fan configuration in the air handling unit and a possible leakage in the heat recovery system. Guidelines were proposed for the design and construction of systems to enable rapid modification of systems in the event of unusual contamination or pathogens in the indoor air.