In most animals, the mucosal immune system effectively controls expression of active immune responses to pathogen and tolerance to harmless antigens. Our understanding of the function and control of the mucosal immune system has advanced as a result of studies in rodents and humans. The discoveries of regulatory T-cells and T-helper-17 cells, and studies on the interactions between epithelial and dendritic cells, demonstrate its complexity. In pigs, some of the systems and reagents for determining the relevance of these mechanisms are present, and indicate lines for future work. However, many empirical studies of the effect of manipulation of the mucosal immune system in the pig by prebiotics, probiotics and feed additives have been carried out. Interpretation of these results needs to be made with care, since manipulation of the mucosal immune system may improve its efficiency under a specific set of environmental and husbandry conditions, but impair it under others.