The purpose of the immune system is not only to fight off pathogens but also to keep a tolerance to self-antigens. In central tolerance, major mechanisms include apoptosis (for T cells) and receptor editing (for B cells). Regulatory T cells appear to be the most important in peripheral tolerance. Innate immune cells also influence the maintenance of immune tolerance. We have provided an overall review of all these mechanisms. Successful restoration of the immune tolerance is the target of new strategies in autoimmune diseases therapy.