There is currently great interest in developing mucosal vaccines against a variety of microbial pathogens. Vaccine delivery systems can target respiratory or intestinal mucosal tissue and stimulate immune response and be particularly effective against these infections. In a healthy human adult, mucosal immune system contributes almost 80% of all immunocytes. The administration of mucosal vaccines does not require the use of needles, increasing vaccine compliance, reducing logistical burden, and minimizing the risks of blood transmissible infections.The primary reason for using a mucosal route of vaccination is that most infections affect or start from mucosal surfaces and that in these infections, topical application of a vaccine is often required to induce a protective immune response both innate and adaptive at the site of pathogen entry. Immunoprophylaxis by the mucosal route is an important approach to controlling mucosally acquired infections. The ability to induce a balanced systemic and secretory immune response following immunization is determined by a complex set of interacting factors. These include the nature of the antigens and route of administration, the nature of the mucosal microenvironment, the immunologic vehicles employed for vaccine delivery, and the effects of bystander immunologic and antigen-related events occurring concurrently in the mucosal environment.