Mitochondrial encephalomyopathies are disorders due to biochemical defects in the respiratory chain, which is under dual genetic control: 13 proteins are encoded by mitochondrial DNA (mtDNA), while all others are encoded by nuclear DNA. In the past 12 years, the small circle of mtDNA has proven to be a Pandora's box of pathogenic mutations, associated with a bewildering variety of multisystemic or tissue-specific disorders. After summarizing the principles of mitochondrial genetics, we attempt to provide general principles and practical clues to the diagnosis of mtDNA-related disorders by reviewing sequentially clinical presentation, family history, laboratory data, neuroradiology, exercise physiology, muscle morphology, muscle biochemistry, and molecular genetics.