Inherited mitochondrial disorders are a group of diseases caused by mutations in mitochondrial DNA (mtDNA) and/or nuclear DNA which encode mitochondria proteins. Nearly every organ and tissue could be affected by mitochondrial disorders, although the neural system and the liver are the most common target organs. Since mtDNA encodes 13 proteins of the respiratory chain, most mutations of mtDNA would result in primary defects of respiratory chain function. There are more than 20 diseases caused by inherited mitochondrial dysfunction, and many of these diseases are either lethal or result in a shortened life span and dysfunctional organs. Mitochondrial dysfunction could also be caused by acquired damage to mitochondria. The electron transport system, especially the respiratory complexes, are frequent targets. Acquired mitochondrial defects are usually caused by toxins, medications, or aging, and are observed in numerous diseases and pathologies including chronic kidney diseases, uremia, cardiac infarctions, cardiac surgery, atherosclerosis, organ transplantations, strokes, spinal cord injury, traumatic brain injury, obesity, diabetes, insulin resistance, as well as age-related disorders such as Alzheimer’s and Parkinson’s diseases, and various types of cancers.