Mitochondrial function can be manipulated selectively by targeting bioactive compounds to mitochondria in living cells. Current targeting mechanisms involve harnessing either the mitochondrial membrane potential or the mitochondrial protein-import machinery to take up molecules linked to lipophilic cations or mitochondrial signal peptides, respectively. Compounds localized like this have been used in studies of mitochondrial metabolism and show potential as anticancer drugs. In addition, because mitochondria play a role in many critical cell processes, mitochondrial targeting has the potential to protect, repair or kill cells selectively, and may become a key tool in the development of gene therapy for mitochondrial DNA diseases.