Airway and digestive tissues are the frontlines of the body's defense, being continuously exposed to the outside environment and encountering large numbers of antigens and microorganisms. To achieve immunosurveillance and immunological homeostasis in the harsh environments of the mucosal surfaces, the mucosal immune system tightly regulates a state of opposing but harmonized immune activation and quiescence. Recently, accumulating evidence has revealed that although the respiratory and intestinal immune systems share common mucosa-associated immunological features that are different from those of the systemic immune system, they also show distinctive immunological phenotypes, functions, and developmental pathways. We describe here the common and distinct immunological features of respiratory and intestinal immune systems and its application to the development of mucosal vaccines.