Inactivation of viable bioaerosol particles, especially stress-resistant microorganisms, has important implications for biodefense and air quality control. It has earlier been shown that the loss of viability of bacterial endospores due to exposure to dry heat is associated with mutational damage. Previous studies, however, used non-aerosolized spores, long exposure times, and moderately elevated temperatures. This study was designed to investigate the mechanism of inactivation of aerosolized Bacillus endospores exposed to high temperatures for sub-second time periods. Bioaerosol was tested in a continuous air flow chamber under two flow rates, 18 L/min and 36 L/min. The chamber had a cylindrical electric heating element installed along its axis. The estimated characteristic exposure temperature (Texposure ) ranged from 164°C to 277°C (with an uncertainty of 21–26°C). To quantify mutational frequency, spores were cultivated after dry heat exposure on tryptic-soy agar and on antibiotic nalidixic acid media. Increases in the exposure temperature caused viability loss and increase in mutational frequency of the spore DNA. Significant association was found between the inactivation factor and the mutational frequency ratio (heat exposed versus non-exposed) with R2 of 0.985 for both flow rates combined. The results suggest that mutational damage is involved in the causal chain of events leading to inactivation of aerosolized endospores exposed to heat for sub-second time periods.