Apoptotic cell death of inflammatory T cells is an established mechanism to terminate an autoimmune inflammatory response in the rodent and human central nervous system (CNS). The efficient clearance of apoptotic cells protects the tissue from leakage of potentially harmful substances from secondary necrotic cells. As the resident phagocyte, the microglial cell is the primary candidate for the clearance of apoptotic lymphocytes. Furthermore, the phagocytosis of apoptotic cells is accompanied by a spectrum of anti-inflammatory effects. In this review, we focus on the mechanisms for removal of apoptotic inflammatory cells by microglia in the central nervous system and their functional consequences.