Mitochondrial dysfunction should be considered in the differential diagnosis of any progressive multisystem disorder. The diagnosis is most challenging when only one symptom is present. In contrast, the diagnosis is easier to consider when two or more seemingly unrelated symptoms are present, involving more than one organ system. It is important to consider the diagnosis of a mitochondrial disorder when dealing with an unexplained association of symptoms, with an early onset and progressive course involving seemingly unrelated organs. The investigation can be relatively straightforward if a person has a recognizable phenotype and if it is possible to identify a known pathogenic mtDNA mutation. The difficulty arises when no known mtDNA defect can be found or when the clinical abnormalities are complex and not easily matched to those of more common mitochondrial disorders. In summary: A full mitochondrial evaluation often is warranted in children with a complex neurologic picture or a single neurologic symptom and other system involvement. When the presentation is classic for a maternally inherited mitochondrial syndrome, such as MELAS, MERRF, or Leber's hereditary optic neuropathy, appropriate mtDNA studies should be obtained first. When the clinical picture is classic for a nuclear DNA inherited syndrome and the gene or linkage is known, such as MNGIE, the clinician should proceed with genetic studies. When the clinical picture is nonspecific but highly suggestive of a mitochondrial disorder, the clinician should start with plasma or CSF lactic acid, ketone bodies, plasma acylcarnitines, and urinary organic acids. If these studies are abnormal, the clinician should proceed with muscle biopsy and assessment of the respiratory chain enzymes. Normal plasma or CSF lactic acid does not rule out a mitochondrial disorder.