Mitochondria are deeply involved in cell fate decisions via their multiple roles in metabolism, cell growth, and cell death. In healthy cells, these functions are highly regulated to provide sufficient energy for cell function, maintain cell homeostasis, and avoid undesirable cell death. This is achieved by an orchestrated cooperation of cellular and molecular mechanisms such as mitochondrial mass control (mitophagy vs biogenesis), oxidative phosphorylation, redox and calcium homeostasis, and the balance between pro- and antiapoptotic proteins. In the 1990s, mitochondria have been demonstrated to directly control some forms of regulated cell death as well indirectly through energetic metabolism modulation. However, a large body of literature revealed that distinct cell death modalities can coexist in vivo as well as that mitochondria can be dispensable for certain forms of cell death. Likewise, unexpected interconnections between cell death pathways can lead to an amplification of lethality, as well as a defeat of cell death resistance mechanisms. This revealed a complexity of the control of cell fate and a crucial need to reevaluate the role of mitochondria. Here, we will review the various cell death pathways such as apoptosis and mitochondrial permeability transition-driven necrosis and discuss how mitochondrial proteins and mitophagy regulate them. Finally, the role of mitochondrial proteins in the triggering of cell death and mitophagy in pathological models, such as cardiac and brain pathologies, will be highlighted. This may help to define efficient cytoprotective therapeutic strategies based on the targeting of mitochondria. © 2016 Elsevier Inc.