A well-functioning immune system is required for proper protection from infections and diseases. Vertebrates have coevolved a comprehensive immune network with the numerous microbes colonizing every surface of their body, particularly in the digestive tract. As such, the immune system has to be trained to discriminate pathogens from symbiotic microbes as well as self from nonself. Commensal microbiota in the gut plays a critical role in this development. Investigations have found correlations of gut microbiota with the development and maturation of a number of components of innate and adaptive immunity. Disruption of this microbiota-host dialog may lead to immune disorders such as allergy and immune-mediated inflammatory diseases.