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Context: Exposure to bio-aerosols in a variety of environments has been of great interest due to the health effects on humans. Hospitals can be the reservoir of these biological agents because of the presence of infectious patients; which can lead to hospital infections and various occupational hazards. In this way, we assessed bacterial contamination in two teaching hospitals in Tehran. Aims: Our purpose in this study assessment of bacterial pathogens and their antibiotic resistance in the air of different wards of selected teaching hospitals in Tehran. Settings and Design: In this study, sampling was done according to NIOSH 0800. Methods and Material: This descriptive study was carried out in the different sections of two hospitals in Tehran. A total of 180 air samples were evaluated according to NIOSH 0800. In each section sampling was performed on the culture media in three stations including primary room, end room, and nursing position then the number of colonies counted. The zone of inhibition was measured in antibiotic disks to determine antibiotic resistance of samples. Statistical Analysis Used: Data analysis was performed using SPSS version 21. Initially, the data were normalized using the Kolmogorov–Smirnov test. The difference between the two hospitals was achieved with Mann–Whitney U test for un-normal distribution data. Results: Bacterial contamination in hospital 2 was significantly higher than the hospital 1(P < 0.001). The median number of colonies in hospital 1 was 129.87 (87.46–268.97) CFU/m3 and 297.97 (217.66–431.85) CFU/m3 for hospital 2. Bacterial contamination in the all of stations in hospital 2 and 87% of samples in hospital 1 was higher than the acceptable range of ACGIH (75 CFU/m3). Conclusions: High bacterial contamination may be related to a lack of hygiene management and poor ventilation system. It seems effective infection control processes, appropriate ventilation systems and supervision systems should be improved.