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Cell turnover is an integral part of embryonic and postnatal development, as well as routine tissue homeostasis, as our bodies replace billions of cells every day. This process involves induction of programmed cell death followed by recognition and removal of the dying cells by phagocytes; but our knowledge of how these steps are regulated is limited. This Collection delivers an overview of current advances in programmed cell death and clearance in the context of tissue homeostasis and injury. It gathers studies investigating molecular regulation mechanisms and implications for conditions including autoimmunity and cancer, as well as research Articles introducing tools for monitoring cell death and clearance.