Isolated mitochondria are an invaluable analytical tool to probe mitochondrial function and evaluate apoptosis induction via the so-called mitochondrial pathway. Irrespective of their tissue origin (e.g., heart, liver, muscle, brain), these organelles participate actively to cell and life decision by producing energy for cell metabolism, but also by undergoing a lethal and irreversible mitochondrial membrane permeabilization (MMP) in stress and pathological conditions. MMP consequences consist, at least in part, in loss of mitochondrial transmembrane potential (ΔΨm), matrix swelling, arrest of respiration and ATP production, and cytochrome c release from the intermembrane space to the cytosol. These parameters can be evaluated in vitro via several miniaturized assays, which have tremendous applications in the field of pharmacology, toxicology, diagnosis, as well as drug discovery.