Mitochondrial encephalomyopathies can be caused by defects in the mitochondrial respiratory complexes. The clinical phenotypes are quite protean but in many instances a characteristic or suggestive clinical presentation permits a tentative bedside diagnosis. The diagnosis can be verified by laboratory investigations. The major laboratory hallmarks of mitochondrial encephalomyopathies include: ragged red fibers on muscle biopsy, a specific defect or deficiency in a mitochondrial respiratory enzyme complex, mtDNA abnormalities, reduced anaerobic threshold by bicycle ergometry, impaired cellular energy state by MRS and characteristic brain imaging abnormalities. Monitoring of some of these parameters along with the clinical phenotype will aid in the evaluation of therapeutic trials.