Mitochondrial DNA (mtDNA) is essential for the aerobic ATP synthesis system that is responsible for about 80% of normal cellular energy demands. In addition to rare genetic disorders causing neuromyopathy, alterations of mtDNA have been found also in so-called common diseases such as heart failure, diabetes, and cancer. Although some of these alterations are inherited, some are considered to be generated and/or accumulated in somatic cells with age. One reason for the somatic mutations is that mtDNA is more vulnerable than is nuclear DNA. For example, mitochondrial respiratory chain produces a large amount of reactive oxygen species as inevitable byproducts of oxidative phosphorylation. However, the molecular mechanisms for maintenance of mitochondrial genome are much less elucidated than those for nuclear genome. In spite of its increasing importance, the molecular diagnosis of mitochondrial DNA-related diseases is well done only in very limited expert laboratories. In this chapter, we focus on maintenance of mtDNA in somatic cells, its clinical importance, and recent developments of molecular tests.