BACKGROUND: The study was planned to show the status of indoor microorganisms and the status of the reduction device in the military dog clinic. METHODS: Airborne microbes were analyzed according to the number of daily patient canines. For identification of bacteria, sampled bacteria was identified using VITEK®2 and molecular method. The status of indoor microorganisms according to the operation of the ventilation system was analyzed. RESULTS: Airborne bacteria and fungi concentrations were 1000.6 ± 800.7 CFU/m(3) and 324.7 ± 245.8 CFU/m(3). In the analysis using automated identification system, based on fluorescence biochemical test, VITEK®2, mainly human pathogenic bacteria were identified. The three most frequently isolated genera were Kocuria (26.6%), Staphylococcus (24.48%), and Granulicatella (12.7%). The results analyzed by molecular method were detected in the order of Kocuria (22.6%), followed by Macrococcus (18.1%), Glutamicibacter (11.1%), and so on. When the ventilation system was operated appropriately, the airborne bacteria and fungi level were significantly decreased. CONCLUSION: Airborne bacteria in the clinic tend to increase with the number of canines. Human pathogenic bacteria were mainly detected in VITEK®2, and relatively various bacteria were detected in molecular analysis. A decrease in the level of bacteria and fungi was observed with proper operation of the ventilation system.