As inductive tissues for the initiation of antigen-specific T and B cell responses, the various mucosa-associated lymphoid tissues (MALT) of the aerodigestive tract, which include gut-associated lymphoid tissue (GALT), nasopharynx-associated lymphoid tissue (NALT) and bronchus-associated lymphoid tissue (BALT), share many histological and immunological characteristics. However, recent advances in our molecular and cellular understanding of immunological development have revealed that the various types of MALT also exhibit different molecular and cellular interactions for their organogenesis. In this review, we delineate the distinctive features of GALT, NALT and BALT and seek to show the role played by those features in the regulation of mucosal tissue organogenesis, the mucosal immune system, and mucosal homeostasis, all in an attempt to provide insights which might lead to a prospective mucosal vaccine.