The accurate diagnosis and classification of mitochondrial diseases are essential first steps in understanding the natural history and true health care burden imposed by these protean and devastating disorders. Epidemiologic studies place the incidence of genetic forms of mitochondrial disease between 1 in 2000 and 1 in 5000 live births. Symptoms may not appear for years after birth, even when inherited. Once they occur, however, the course is often relentlessly progressive. Diagnosis requires a combination of clinical and laboratory studies that are applied systematically. DNA analysis and respiratory chain studies remain the mainstays of diagnosis, but several other disciplines may contribute to achieving diagnostic confidence when a single study is suggestive but inconclusive. A comprehensive classification system for mitochondrial diseases has not yet been developed. The current International Classification of Diseases, 10th Revision (ICD-10) includes just 10 codes for mitochondrial disorders. Supplementary data of 347 proposed ICD-10 codes is included to assist with the development of a more comprehensive system for the diagnosis and classification of mitochondrial disease.