Mitochondria play a key role in cell death and its regulation. The permeabilization of the outer mitochondrial membrane which is mainly controlled by proteins of the BCL-2 family, is a key event that can be directly induced by p53 and results in the release of pro-apoptotic factors to the cytosol, such as cytochrome c, second mitochondria derived activator of caspases/direct inhibitor-of-apoptosis (IAP) binding protein with low pI (SMAC/Diablo), Omi serine protease (Omi/HtrA2), apoptosis inducing factor (AIF), or endonuclease G (Endo-G). Hence, the determination of subcellular localization of these proteins is extremely important to predict cell fate and elucidate the specific mechanism of apoptosis. Here we describe the procedures that can be used to study the subcellular location of different pro-apoptotic proteins to be used in basic cell biology and toxicology studies.