The gut-associated lymphoid tissue is deputed both to protect from infectious diseases and to evoke immune tolerance. Efficient responses need mucosal adjuvants: starting from cholera toxin, new variants of cholera toxin were developed depleted of toxicity. In addition, lipid colloidal particles, bacterial DNA, and probiotics have been experimented. Tolerance is currently induced by means of the B subunit of cholera toxin, whereas new strategies encompass the use of probiotics, expansion of regulatory T cells and blocking of paracellular entry of antigens. Finally, we report different approaches developed for celiac disease, an immune-mediated disease whose triggering antigen is known.