Airborne biological agents, albeit intentionally released or naturally occurring, pose one of the biggest threats to public health and security. In this study, a microwave assisted nanofibrous air filtration system was developed to disinfect air containing airborne pathogens. Aerosolized E. coli vegetative cells and B. subtilis endospores, as benign surrogates of pathogens, were collected on nanofibrous filters and treated by microwave irradiation. Both static on-filter and dynamic in-flight tests were carried out. Results showed that E. coli cells were efficiently disinfected in both static and in-flight tests, whereas B. subtilis endospores were more resistant to this treatment. Microwave power level was found to be the major factor determining the effectiveness of disinfection. Both thermal and non-thermal effects of microwave irradiation contributed to the disinfection. Reducing flow velocity to decrease heat loss yielded higher disinfection efficiency. (C) 2010 Elsevier Ltd. All rights reserved.