Mitochondrial genome integrity is an important issue in somatic mitochondrial genetics. Development of quantitative methods is indispensable to somatic mitochondrial genetics as quantitative studies are required to characterize heteroplasmy and mutation processes, as well as their effects on phenotypic developments. This chapter outlines the methods for collecting individual cells appropriate for analysis of mtDNA mutations by single-molecule PCR. In addition, we describe the protocols for respiratory complexes II and IV in these cells. Together, the identification of respiratory deficiency and mtDNA mutations within single cells provides a powerful means of evaluating the importance of these events in disease and aging.
