This review discusses the mechanisms, pathophysiological roles, and assays used to monitor mitophagy. Mitophagy is the process of removing damaged mitochondria through autophagy, which is crucial for maintaining cellular functions. The induction of mitophagy involves two steps: the induction of general autophagy and the priming of damaged mitochondria for selective autophagic recognition. Mitochondrial priming can be mediated by the Pink1-Parkin signaling pathway or the mitophagic receptors Nix and Bnip3. Recent studies have revealed that mitochondrial fragmentation facilitates mitophagy, and multiple molecules and pathways regulate mitochondrial homeostasis. The review also discusses the role of mitophagy in development, aging, cancer, neurodegenerative diseases, and innate immunity. Key players in mitophagy include Atg32, Uth1p, Aup1p, Atg11, Atg19, Atg5, Atg8/LC3, ULK1, Beclin 1, p62, Nix, Bnip3, FUNDC1, SMURF1, HMGB1, Hsp90-Cdc37, Atg9A, ULK1, and 15-lipoxygenase.This review discusses the mechanisms, pathophysiological roles, and assays used to monitor mitophagy. Mitophagy is the process of removing damaged mitochondria through autophagy, which is crucial for maintaining cellular functions. The induction of mitophagy involves two steps: the induction of general autophagy and the priming of damaged mitochondria for selective autophagic recognition. Mitochondrial priming can be mediated by the Pink1-Parkin signaling pathway or the mitophagic receptors Nix and Bnip3. Recent studies have revealed that mitochondrial fragmentation facilitates mitophagy, and multiple molecules and pathways regulate mitochondrial homeostasis. The review also discusses the role of mitophagy in development, aging, cancer, neurodegenerative diseases, and innate immunity. Key players in mitophagy include Atg32, Uth1p, Aup1p, Atg11, Atg19, Atg5, Atg8/LC3, ULK1, Beclin 1, p62, Nix, Bnip3, FUNDC1, SMURF1, HMGB1, Hsp90-Cdc37, Atg9A, ULK1, and 15-lipoxygenase.