Tolerance to self and harmless antigens is one of the central features of the immune system, and it is obtained through a combination of multiple mechanisms. Discriminating between pathogens and non-pathogenic antigens is especially important in the intestine, which constitutes the main contact surface between the body and the outside environment. Recently, the role of Foxp3+ regulatory T cells (Treg) in the establishment and maintenance of tolerance has been the focus of numerous studies. In this review, we briefly discuss the historical background leading to the identification of Foxp3+ Treg and give an overview of their role in controlling systemic and mucosal immune responses.