The complex interactions between the GI tract microbiota and the immune system can be simplified for study using gnotobiotic animal models. The importance of cytokines, such as IFN-gamma, TNF-alpha, TGF-beta, Interleukin-2, IL-4 and IL-10 in the host response to intestinal bacteria has been evaluated using gnotobiotic studies. Gnotobiotic experiments with immunodeficient animals have revealed insights into the relationships between innate, cell-mediated and antibody-mediated immune system components in resistance to infectious microorganisms. The development and maturation of the immune system is dependent on the presence of some members of the intestinal microbiota. The commensal microorganisms, in turn, are dependent on the environment and nutrients provided by the GI tract of the host. Gnotobiotic studies are starting to reveal how the microbiota influences oral tolerance to dietary and commensal bacterial antigens. The immunomodulatory effects of microbiota and probiotics for inflammatory bowel diseases and the role of bacteria in their etiologies are being studied in gnotobiotic systems. Many aspects of the host interaction with the microbiota have been and will continue to be best addressed in gnotobiotic experimental models. This chapter reviews the contributions that gnotobiology has made to our understanding of the microbiota and host GI tract health.