A child is born with almost no protective immune system other than passive immunity and maternal transfer of immunoglobulin G (IgG) against various food antigens and infectious agents. This lack provides a window of opportunity for infectious attacks in the first 6 mo of life as the infant’s body begins to develop its own immune system. As the maternal IgG is catabolized, the child’s mucosal immune system evolves its own immunocytes and starts producing a significant amount of immunoglobulin A (IgA) and immunoglobulin M (IgM) against pathogens and food antigens. This antibody production helps modulate or inhibit colonization by bacteria or yeast and to prevent penetration of the mucosal tissue by a variety of dangerous lumenal antigens. Simultaneously, the body develops its own suppressive mechanism or oral tolerance to avoid local and peripheral immune reactivities to microbial and dietary antigens. In this article, the author describes the (1) importance of oral tolerance in maintaining homeostasis against bacterial toxins and food antigens; (2) way in which antigen-presenting cells (APCs), through their collaboration with effector T (TEFF) cells, T-helper (TH) cells, and regulatory T (TREG) cells, regulate the immune system to induce anergy or immune suppression; (3) the importance of various factors in the induction of oral tolerance and the consequences of its breakdown; and (4) the reasons why a disruption of oral tolerance to food antigens and bacterial toxins can result in autoimmunity.