Associated with the intestine is a well developed local immune system that is dependent upon the establishment of a gut microbial flora for its development. The gut mucosal immune system is required to recognize and respond “appropriately” to different groups of antigens via a vigorous response to potential pathogens and by not overreacting to otherwise harmless dietary antigens. The high incidence of food allergic reactions and paucity of mucosal vaccines highlight the difficulties associated with controlling and targeting these responses.