Gut-resident forkhead box P3 (FOXP3)⁺CD4⁺ regulatory T cells (T_reg cells) are distinct from those in other organs and have gut-specific phenotypes and functions. Whereas T_reg cells in other organs have T cell receptors (TCRs) specific for self antigens, intestinal T_reg cells have a distinct set of TCRs that are specific for intestinal antigens, and these cells have pivotal roles in the suppression of immune responses against harmless dietary antigens and commensal microorganisms. The differentiation, migration and maintenance of intestinal T_reg cells are controlled by specific signals from the local environment. In particular, certain members of the microbiota continuously provide antigens and immunoregulatory small molecules that modulate intestinal T_reg cells. Understanding the development and the maintenance of intestinal T_reg cells provides important insights into disease-relevant host–microorganism interactions.