The Bcl-2 proteins are best known as regulators of the intrinsic mitochondrial pathway of apoptosis. However, recent studies have demonstrated that they can also regulate autophagy. For many years, autophagy was considered to be a nonselective process where the autophagosomes randomly sequestered contents in the cytosol to supply the cells with amino acids and fatty acids during nutrient deprivation. However, it is now clear that autophagy is important for cellular homeostasis under normal conditions, and that it can be a selective process where specific protein aggregates or organelles, such as mitochondria, are targeted for removal by the autophagosomes. Removal of damaged mitochondria is essential for cellular survival, and defects in this process lead to accumulation of dysfunctional mitochondria and cell death. However, the molecular mechanism underlying the selective removal of mitochondria in cells is still poorly understood. A recent study from our laboratory demonstrates that the BH3-only protein Bnip3 is a specific activator of mitochondrial autophagy (mitophagy) and that this process is independent of its role in apoptotic signaling. Here, we discuss how Bnip3-mediated impairment of mitochondrial oxidative phosphorylation facilitates mitochondrial turnover via autophagy in the absence of permeabilization of the mitochondrial membrane and apoptosis.