The subject of this article is the evaluation of operation and maintenance of the existing ventilation systems in Slovakia in terms of microbiological contamination. The methodology of microbiological survey was chosen for the purpose of research, air samples, samples from the surface and water samples was collected and evaluated. In conclusion, the results of air contamination and surface contamination of the ventilation systems are processed graphically. The aim of this work is to show the air-conditioning units and air conducts as potential sources of microbiological pollution in the building internal environment.