Exposure to bioaerosol from the premises of veterinary clinics poses a significant threat to the health of veterinary staff and patient animals. Because pathogens of airborne infections can be transmitted through it. The aim of the work was to determine the number of mesophilic aerobic microorganisms in the bioaerosol of various premises of veterinary clinics during their operation and under the influence of disinfection. Bioaerosol samples were collected in the premises of veterinary clinics using the sedimentation method. The seeded Petri dishes were placed in a thermostat at an incubation temperature of +37 ± 1 °C for 48 hours. It was established that the number of mesophilic microorganisms in the bioaerosol of veterinary clinics was the highest in the room for primary examination, in the manipulation area with boxes for keeping sick animals and in the dental operating room – from 1943.5 ± 127.1 to 2725.2 ± 193.4 CFU/m3. That is, in no room was an excess of the number of bacteria in the bioaerosol found in accordance with the conditional standard of 5000 CFU/m3. Although in other premises of these veterinary clinics, the number of mesophilic microorganisms in the bioaerosol was much lower and ranged from 102.4 ± 8.3 to 123.1 ± 9.5 CFU/m3. It was found that in the rooms for the primary examination, the manipulation area with boxes for keeping sick animals and in the dental operating room, in the bioaerosol with the maximum number of mesophilic microorganisms (from 2801.3 ± 178.2 to 1605.4 ± 127.3 CFU/m3) in the winter period, the number of bacteria was 1.5 times higher, compared to the content in the summer period. Therefore, in winter, the “pressure” of bioaerosol microbiota increases on veterinary staff and animal patients, which in turn can lead to the transmission of pathogens by airborne droplets. During the assessment of preventive measures implemented in veterinary clinics, it was found that in the premises for primary examination, the manipulation area with boxes for keeping sick animals and in the dental operating room, in bioaerosol, which were detected from 1193.5 ± 107.4 to 1885.1 ± 119.4 CFU/m3 of mesophilic microorganisms after one-hour treatment with bactericidal lamps, the number of microbiota decreased by 13.1–15.4 times. At the same time, in rooms where microbial air pollution before disinfection was within the range of 130.6 ± 7.8−223.9 ± 14.1 CFU/m3, after exposure to ultraviolet radiation, the content of bacteria decreased by 3.7–4.7 times. That is, in the bioaerosol of all rooms, there remains a stable part of the microbiota in the amount of 30–150 bacteria per m3, which was not exposed to the bactericidal effect of the lamps. Therefore, determining the risk of spreading bioaerosol pathogens in veterinary clinics will make it possible to implement sanitary and epidemiological measures to reduce the transmission of pathogens in a timely manner.