In this study, the dog, cat allergens (Can f 1 and Fel d 1) and fungal allergens (Alt a 1 and Asp f 1) were aerosolized and exposed to the microwave irradiation (2450 MHz) at different output powers for up to 2 min. The allergen bioaerosols were collected by a BioSampler, and analyzed using enzyme-linked immunosorbent assay (ELISA). Control and microwave-irradiated Asp f 1 allergens were also tested with IgEs in human blood sera samples. For airborne Asp f 1 and Alt a 1 allergens, the allergenicity was shown to decrease about 50% when exposed to microwave irradiation at 385 and 119 W and relatively no change at 700 W. For airborne Can f 1 allergen, the allergenicity was shown to increase about 70% when exposed to the irradiation at 385 W, but remained relatively unchanged at 700 and 119 W. In contrast, airborne Fel d 1 allergen was observed to lose allergenicity completely at 700 W, and retained about 40% and 80% at 385 and 119 W, respectively. Radioallergosorbent (RAST) tests showed that changes detected in IgE levels in human blood sera mixtures were not statistically significant for the control and microwave-irradiated waterborne Asp f 1 allergens. This study implies that although certain allergenicity reductions were observed for some allergens in certain cases, particular care should be taken when the microwave irradiation is used to disinfect food, water, and air because of its complex effects.