The present invention provides a therapeutic method for the treatment of autoimmune or autoinflammatory diseases by first breaking down the dysregulated immune system and then reprogramming the immune system to restore tolerance to the patient's self-antigens by induction of antigen specific regulatory T cells. The inventors have shown that only with the combination of apoptosis, phagocytes, and antigen can antigen-specific regulatory T cells (T_reg) cells be optimally generated to develop long-term immune tolerance. This strategy for developing immune tolerance can be applied to the treatment of autoimmune diseases.