Mitochondrial diseases have extremely heterogeneous clinical presentations due to the ubiquitous nature of mitochondria and the dual genetic control of the respiratory chain. Thus, mitochondrial disorders can be multisystemic (mitochondrial encephalomyopathies) or confined to a single tissue, and they can be sporadic or transmitted by mendelian or maternal inheritance. Mendelian disorders are usually inherited as autosomal recessive traits, tend to present earlier in life, and usually "breed true" in each family. By contrast, mitochondrial DNA-related diseases usually start later and vary in their presentation within members of the same family. Precise diagnosis is often a challenge; we go through the traditional steps of the diagnostic process, trying to highlight clues to mitochondrial dysfunction in the family history, physical and neurological examinations, routine and special laboratory tests, and histo-chemical and biochemical results of the muscle biopsy. The ultimate goal is to reach, whenever possible, a definitive molecular diagnosis, which permits rational genetic counseling and a prenatal diagnosis.