Transition metal ions are required for many aspects of mitochondrial physiology. Copper, iron, manganese and zinc are cofactors in metalloenzymes and metalloproteins within the organelle. Little is known how cells maintain optimal pools of these metal ions for mitochondrial function. This review documents the available literature on mitochondrial metal ion pools and protein metallation reactions. Upon perturbation in metal pools, mis-metallation reactions do occur. Thus, regulation of metal ion accessibility and bioavailability must exist.