In and around poultry farms, high concentrations of endotoxins are found that have a negative impact on the health of farmers and local residents. However, little is known about the effects of chronic exposure to endotoxins on the health of poultry. The aim of this study was to identify effects of chronic exposure to airborne endotoxins (E. coli LPS) on the immune system, respiratory tract, disease susceptibility and welfare of broilers. Effects of high (HE) and low endotoxin (LE) concentrations on natural antibody titers (NAb), performance and behavior of broilers were determined. After treatment with a respiratory virus infection, infectious bronchitis virus (IBV), mRNA expression of cytokines and Toll-like receptor (TLR) 4 in the lung, tracheal ciliary activity and lesions in the respiratory tract were determined. Endotoxin affected the immune system and respiratory tract, where HE broilers tended to have lower IgM NAb binding Phosphorylcholine-conjugated to Bovine Serum Albumin, and higher interferon (IFN)-α mRNA expression and more lesions in the nasal tissue compared to LE broilers. Furthermore, HE broilers had higher TLR4 mRNA expression compared to LE broilers. However, endotoxin did not affect NAb levels binding Keyhole Limpet Hemocyanin, IFN-β and interleukin-10 mRNA expression, IBV replication or lesions in the lung and trachea. HE and LE broilers further had similar body weight, but HE broilers showed numerically more passive behavior compared to LE broilers. In conclusion, chronic exposure to high airborne endotoxin concentrations affects components of the immune system and respiratory tract in broilers and could therefore influence disease susceptibility.