Apoptosis and the rapid clearance of apoptotic cells by professional or nonprofessional phagocytes are normal and coordinated processes that ensure controlled cell growth with a nonpathological outcome. Defects in clearance of apoptotic cells by macrophages have serious consequences often resulting in autoimmune disorders. Phagocyte-derived immunoregulatory cytokines such as Interleukin-12 and Interleukin-10 play pivotal roles in the etiology and pathology of many autoimmune diseases. Elucidation of the apoptotic cell-mediated signaling mechanisms involved in the control of pro- and anti-inflammatory cytokines during cell turnovers under normal and pathological conditions may help us counter the cytokine dysregulation and control inappropriate host immune reactions in pathological situations such as autoimmunity, infectious diseases, graft-versus-host disease, and cancer.