Mucosal microbiota and antigens of external environment are the most important stimuli which contribute to the development and induction of immune responses in the entire immune system. Intimate and mutually beneficial co-existence of higher organisms with enormously diverse mucosal microbita is dependent on the complementary interactions of innate and specific immunity. Interventions and changes in mucosal microbiota which influences the immune system may result in its consequences such as the development of several diseases associated with mucosal tissues including allergies, but also organ specific and systemic diseases. It has been convincingly demonstrated that T regulatory cells play the central role and direct through their products antibody responses of diverse isotypes, the expression of receptors with ensuing activation of cells involved in allergic reactions. The characterization of microbial components and elucidation of underlying molecular mechanisms that participate in pathologic or health-promoting effects can substantially influence the composition of mucosal microbiota and lead to the identification of components whose application may result in the prevention and treatment of immunologically-mediated diseases.