Diagnosis of mitochondrial disorders has been difficult due to the clinical and genetic heterogeneity, as well as unique features of mitochondrial genetics. Definitive diagnosis requires the identification of molecular defects in either the mitochondrial or the nuclear genome. We describe the clinical symptoms characteristic of certain mitochon-drial syndromes and PCR-based methodologies available for the detection of known common point mutations. Several indirect methods for the detection of unknown mutations are also described. Large deletions can be detected by Southern blot analysis. The utility of real time quantitative PCR in the determination of mitochondrial DNA content is discussed. This review provides overview of current understanding of the molecular genetics of mitochondrial disor-ders that is useful in genetic counseling and molecular testing.