Mucosal surfaces, especially the gastrointestinal (GI) tract, are obligatory sites for tolerance induction against numerous exogenous antigens. Therefore, the mucosal surface seems to provide a microenvironment conductive to the induction of antigen-specific regulatory T cells. The cytokine milieu, which includes IL-10 and TGF-beta, affects effector function of local dendritic cells and induces regulatory T cells (iT(REG)). During immune homeostasis (steady state) in the GI tract, noninflammatory innate immune signals provided by innocuous or commensal bacteria seem to play important roles in the induction of regulatory cytokines that enable the establishment of tolerance, which involves iT(REG) function. In accordance with this viewpoint, utilizing physiological means such as probiotics and TLR ligands may improve the homeostatic conditions of immune-mediated diseases and inflammation. Antigen-specific iT(REG) is a great counterpart of thymus-derived CD25(+)CD4(+)Foxp3(+) T(REG) (nT(REG)), and therefore clinical applications of T(REG) should be developed that integrate the advantages of both of these cell populations. Close investigation of mucosal iT(REG) and related microenvironments not only will facilitate novel interventions of mucosal immunity but also will help to best utilize iT(REG) and iT(REG) in an integrated way.