The epithelial surfaces of the respiratory tract represent a fragile interface between the immune system and the outside environment. In order to maintain local homeostasis, the adaptive immune system must continuously discriminate between innocuous antigens which are ubiquitous in the atmosphere, and antigens associated with microbial pathogens. Any breakdown in this discrimination process can potentially lead to chronic inflammatory disease. The mechanisms employed by the mucosal immune system to maintain this delicate balance are many and varied, and a comprehensive understanding of how they collectively operate would provide novel insight into a wide variety of diseases. This discussion reviews recent progress in this area, focusing on allergic respiratory disease as a model for the study of immune regulation at mucosal surfaces.