The importance of functional mitochondria to the regulation and optimization of the cellular environment is demonstrated by their integral role in fundamental processes such as energy provision, redox status, as well as pH, calcium, and osmotic homeostasis. Several unique structural and functional properties of this organelle offer it as a potential target for the induction of cellular toxicity. Mitochondria are susceptible to damage by various types of agents, including electrophiles, lipophilic cations, and oxidants. The mitochondrial genome, the integrity of which is essential for efficient bioenergetics, is preferentially susceptible to DNA damaging agents; mutations within this genome have the potential to accumulate rapidly as a result of the decreased repair capacity and, lack of genetic recombination characteristic of mtDNA. Mitochondria also maintain an electronegative gradient across their inner membrane, making them a natural sink for lipophilic cationic agents. Several such agents have the potential to dissipate the mitochondrial membrane potential and, in so doing, commit the cell irreversibly to death. Furthermore, the association of the mitochondrial membranes with proteins critical to the stress response give it a central role in mediating growth, division, and apoptotic signals. The important contribution of mitochondria to numerous mechanisms of toxicity and the availability of reliable quantification methods for the basic properties of normal and dysfunctional mitochondria make damage to this organelle a suitable marker for various types of toxicity.