**Abstract**

The pathogenesis of autoimmune diseases (AIDS) is not only attributed to genetic susceptibility, but also to environmental factors, among which, those disturbing gut microbiota have attracted increasing attention lately. Healthy gut microbiota has beneficial effects on the development and activity of the immune system, playing a central role in peripheric tolerance. Compositional and functional changes in gut microbiota were reported in various AIDS, and increasing evidence suggests that disturbed gut microbiota contributes to their immunopathogenesis. Thyroid and intestinal diseases prevalently coexist—for instance, Hashimoto's thyroiditis and Graves' disease are the most common autoimmune thyroid diseases and often co-occur with celiac disease. This association can be at least explained by increased intestinal permeability, allowing antigens to cross the barrier more easily and activate the immune system. The passage of microbial antigens into the internal environment may break the self-tolerance, generating the production of autoantibodies and/or autoreactive T cells. In this chapter, we briefly present the roles of intestinal microbiota in human physiology, with a focus on the role of microbiota in immune tolerance.

**Keywords:** microbiome, gut immunity, dysbiosis, immune tolerance, autoimmunity
