We have known for many years that mucosal responses to antigens are regulated by immune cells and their molecular signals. More recently, it has become clear that epithelial cells also synthesize and secrete chemokines and cytokines. A sophisticated system of bidirectional cytokine signals is responsible for immune activation in the case of enteropathogens vs. immune suppression to food and commensal microbial antigens. A key factor in determining antigen handling is the route taken by antigens across the epithelial barrier. Cytokines and other mucosal messenger molecules play a critical role in the regulation of transepithelial antigen transport.