With increases in large animal-feeding operations to meet consumer demand, adverse upper and lower respiratory health effects in exposed agriculture workers are a concern. The aim of this study was to review large animal confinement feeding operational exposures associated with respiratory disease with a focus on recent advances in the knowledge of causative factors and cellular and immunological mechanisms. A PubMed search was conducted with the keywords airway, farm, swine, dairy, horse, cattle inflammation, organic dust, endotoxin, and peptidoglycan, among items were published between 1980 and now. Articles were selected based on their relevance to environmental exposure and reference to airway diseases. Airway diseases included rhinitis, sinusitis, mucus membrane inflammation syndrome, asthma, chronic bronchitis, chronic obstructive pulmonary disease, hypersensitivity pneumonitis, and organic dust toxic syndrome. There is lower prevalence of immunoglobulin (Ig) E-mediated asthma and atopy in farmers and their children, but organic dust worsens existing asthma. Multiple etiologic factors are linked to disease, including allergens, organic dusts, endotoxins, peptidoglycans, and gases. Large animal confinement feeding operations contain a wide diversity of microbes with increasing focus on gram-positive bacteria and archaebacteria as opposed to gram-negative bacteria in mediating disease. Toll-like receptors (TLR) and nucleotide oligomerization domain (NOD)-like innate immune pathways respond to these exposures. Finally, a chronic inflammatory adaptation, tolerance-like response in chronically exposed workers occurs. Large animal confinement farming exposures produce a wide spectrum of upper and lower respiratory tract diseases due to the complex diversity of organic dust, particulates, microbial cell wall components, and gases and resultant activation of various innate immune receptor signaling pathways.