Mitophagy is a process of selective removal of damaged or unnecessary mitochondria using autophagic machineries. Mitophagy plays an essential role in mitochondria quality control and mitochondria homeostasis. Mitochondria dysfunctions and mitophagy defects in neurodegenerative diseases, cancer, metabolic diseases indicate a close link between human disease and mitophagy activity. Furthermore, recent studies showing the involvement of mitophagy in differentiation and development, suggest that mitophagy may play a more active role in controlling cellular functions. The better understanding of mitophagy will provide insight about human disease and offering novel chance for treatment. This review mainly focuses on the recent implications of mitophagy in human diseases and normal physiology.