The epithelium, including the respiratory system, acts as a selective gate between the outside environment and underlying tissue. Epithelial cells are polarized due to the formation of the apical junctional complex, which includes adherent junctions and tight junctions. Endothelial cells are one of the most important cellular constituents of blood vessels. Endothelial junctional proteins play important roles in tissue integrity as well as in vascular permeability, leukocyte extravasation, and angiogenesis. This review focuses on the apical junctional complex in respiratory diseases.