Mitochondria are vitally important organelles within our cells. In addition to being the key energy provider, they perform numerous other essential roles ranging from calcium homeostasis to iron metabolism. Therefore, these mitochondrial functions are dependent on the quality and number of mitochondria, which needs to be dynamic in response to a cell's changing needs. Mitochondrial numbers themselves are controlled by mitochondrial biogenesis and turnover. Multiple pathways exist that result in the turnover of mitochondria, but the focus of this review will be on mitophagy (the autophagy of mitochondria). Here, we will touch on the basic mechanisms of mitophagy and how this has been translated from cell-based studies to complex mammalian systems. We will then examine the tasks that mitophagy serves in vivo. While mitochondrial quality control is a critical function of mitophagy, we will also discuss the recent roles that mitophagy plays in metabolic remodeling.