Apoptosis serves many functions in the homeostasis of multicellular organisms. Defects in apoptosis may lead to clonal expansion and accumulation of autoreactive lymphocytes, which may result in the rare human autoimmune lymphoproliferative syndrome, a mild autoimmune reaction against cells in the blood. Defects in the clearance of apoptotic cells lead to accumulation of dying cells, which may enter later stages of cell death and release their contents, thereby critically contributing to the etiopathogenesis of the autoimmune disease systemic lupus erythematosus. For an efficient therapy of systemic lupus erythematosus, it is necessary to analyze apoptosis and clearance defects and to unravel factors leading to its onset.