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An aerobiological study was performed to evaluate the potential exposure of animals and workers to dust constituents generated during routine animal house work. Different rooms of air conditioned (A, control) and passively ventilated (B, non-air conditioned) animal facilities were sampled, in order to evaluate total airborne culturable fungi and bacteria, fungal spore concentrations and particle levels. Airborne room particles were analyzed gravimetrically and for endotoxin content. All parameters, except for culturable fungi, were higher in facility B and statistically significant, with respect to those from the control facility A. Median values for airborne particle concentration, endotoxin and fungal spores in facility B were: 115 µg m−3, 25 EU m−3, and 2173 spores m−3, respectively. Median values for facility A were: 66 µg m−3, 9 EU m−3, and 248 fungal spores m−3. Broncheoalveolar lavage from rats kept in the rat room of B, presented median concentrations of total cells and lactate dehydrogenase, higher than those found in the control facility (4.4 × 105vs. 1.1 × 105 and 2.7 UmL-1vs. 0.39 UmL−1, respectively). Values of total and biological particles of both facilities, as well as the time spent in different rooms, showed that worker exposure was higher during cage washing. It was especially high in the passively ventilated facility (airborne particles 686 µg m−3 3.5 h−1vs. 976 µg m−3 3.5 h−1, endotoxin 70 EU m−3 3.5 h−1vs. 108 EU m−3 3.5 h−1). The type of basidiospores and ascospores found, as well as the significant correlation between particle levels and endotoxin contents suggests that wood chip bedding disturbance during cage washing is an important source for airborne biological particles. The changes in broncheoalveolar lavage components found in rats from these facilities and previously reported changes in pro-inflammatory cellular responses found in workers, indicate that these relatively low levels of exposure are enough to induce a biological response. Studies considering the composition of mixed organic dusts, would be needed to reevaluate current occupational standards.