Summary Bioaerosols (aerosols composed of solid particles or liquid droplets measuring 0.002 to 100 µm and carrying live microorganisms or molecules derived from living organisms) are found in high concentrations in a number of work environments. Many occupational respiratory diseases are associated with bioaerosols, but their etiology is often unknown. The exact composition of the bioaerosols responsible for these respiratory diseases must be clearly determined, so we can understand just what workers are exposed to.We recently documented unsuspected microorganisms (archaea) in the air of hog houses. In this study, molecular biology methods are used to describe the biodiversity of bacteria and archaea in the air of a number of work environments so that the bioaerosol exposure of workers can be determined. We thus characterized the bacteria and archaea content of bioaerosols in dairy farms, poultry houses and wastewater treatment plants and determined the exposure of dairy-farm workers to Saccharopolyspora rectivirgula, the agent responsible for farmer’s lung. In addition, we used a mouse model of chronic airway exposure to characterize the immunogenicity of two species of archaea found in the air in different work environments: Methanobrevibacter smithii (MBS) and Methanosphaera stadtmanae (MSS). The polymerase chain reaction (PCR) technique was used to determine quantities of bacteria and archaea in the air in dairy farms, poultry houses and wastewater treatment plants. Denaturing gradient gel electrophoresis (DGGE) was used for biodiversity characterization of these microorganisms. The ELISA technique was used to measure antibodies specific to MBS, MSS and S. rectivirgula in workers’ blood plasma. To study the pro-inflammatory effects of archaea, C57BI/6 mice were instilled intranasally with three different concentrations of two species of archaea (MBS and MSS) for three consecutive days during three weeks. A total of up to 108 bacteria and 106 archaea per m3 were detected in dairy farm air. Similar quantities of archaea were found in poultry house air. A total of up to 108 bacteria and 104 archaea per m3 were found in the air of wastewater treatment plants. MBS and MSS, two species of immunogenic archaea, were also detected in the farm air sampled. Despite recommendations to the farmers regarding storage of their hay, up to 107 copies of the 16S rRNA gene of S. rectivirgula were measured per m3 of farm air. In fact, exposure to this actinomycete was greater in dairy farm workers than in the control group. Histopathological studies of the lungs of mice exposed to archaea demonstrate changes to the lungs, and these were more intense in mice instilled with MSS. The mouse model also made it possible to demonstrate that MSS induces greater production of activated myeloid dendritic cells in the lungs than MBS.These results demonstrate the complexity of bioaerosols in agricultural and industrial environments. Some components of these bioaerosols, such as archaea, may play a role in the development of occupational respiratory diseases. These microorganisms can cause lung inflammation, the intensity depending on the species of archaea. We are just beginning to explore these archaea in our environment and to understand our response to these little known agents. Their role as protective, immunostimulatory, proinflammatory or tolerated agents merits further exploration.