Background: Bacterial agents found in the airways of hospitals and medical centers can be very harmful. In this study, microwave radiation was employed in order to remove Pseudomonas aeruginosa from hospital air. Materials and Methods: Microwave radiation power of 180, 360 and 540 W was used. The bacterial strain used was Pseudomonas aeruginosa (ATCC 27853). Bacterial aerosols in the range of 107 and 106 of bacteria per ml of air, which was prepared using a nebulizer, was injected into the system. Results: The results of this study showed that the number of bacteria remaining in the system decreased with increasing microwave power. There was absolutely no bacterial growth following 240 min of exposure to 540 watt radiation density for 107 bacteria in each ml of air current. Conclusion: Microwave radiation with high functionality can be used to remove bacterial air pollutions. They can help to control biological agents in hospitals and medical centers with good efficiency.