Mucosal immunology is the study of immune system responses that occur at mucosal membranes of the intestines, the urogenital tract and the respiratory system, i.e., surfaces that are in contact with the external environment. In healthy states, the mucosal immune system provides protection against pathogens but maintains a tolerance towards non-harmful commensual microbes and benign environmental substances. It provides three main functions: protecting the mucous membrane against infection; preventing the uptake of antigens, microorganisms, and other foreign materials; and moderating the organism's immune response.
At birth, the neonate's mucosal immune system is relatively undeveloped, but the colonization of intestinal flora promotes its development.
Because of its front-line status within the immune system, the mucosal immune system is being investigated for use in vaccines for various afflictions, including AIDS and allergies.