Endotoxins are widely distributed toxins in the outer cell-wall membranes of Gram-negative bacteria and other microorganisms. Chronic exposure to endotoxins can induce and exacerbate airway symptoms and diseases. However, the release and degradation of airborne endotoxins from bioaerosol by microwave (MW) irradiation have not yet been reported. This study investigated the distribution and fate of airborne endotoxins during MW irradiation process, as well as the kinetics and thermodynamics of the degradation of airborne endotoxins. Results showed that MW irradiation induced cell lysis, thus considerably increasing the proportion of cells with ruptured membranes. Furthermore, MW irradiation changed the distribution of airborne endotoxins, sharply decreased the concentration of bound endotoxins from 230 EU/m(3) to 68 EU/m(3), and increased the concentration of free endotoxins from 21 EU/m(3) to 122 EU/m(3). These results indicated that MW irradiation released endotoxins from cells into the atmosphere. MW irradiation likely degraded endotoxins by exerting thermal effects, which achieved a total endotoxin removal efficiency of as high as 35%. Endotoxin degradation was a first-order reaction and required the activation energy of 26.3 kJ/mol.