The aim of the study was to valuate effectiveness of the air condition system in hospitals. It was done by estimation of bacteria and fungi concentration in the air. The study were performed in ten hospital rooms which were protected by EU 13 or EU 9 filters. Possible the most important source of fungi was not treated air incoming from outside. Only in four of the rooms concentrations of the fungi in the air were satisfactory and not exceeded 20 cfu/m3 (cfu--colony forming unit). However in two of them the number of fungi rise 4-5 times after the windows were opened. Concentration of the fungi in operating theater number 2 (1-2 cfu/m3) allow to valuate efficiency of air conditioning systems. The lowest bacteria concentration was in Intensive Care Unit (73 cfu/m3) but the highest in instrumentalists rum (1427 cfu/m3. where according to high fungi concentration (116 cfu/m3) the air conditioning systems was switched of and the ventilation was by open windows.