Mitochondrial diseases are multiorgan system disorders and the brain is the most commonly affected organ. The high-energy requirement of the brain leaves it vulnerable to energy failure. All components of the neuraxis including muscle, the neuromuscular junction, peripheral nerve, spinal cord, and brain can be affected. Genetic mitochondrial disease can be caused by nuclear gene defects and mitochondrial DNA defects. Mitochondrial medicine is rapidly expanding as exome and mtDNA sequencing is identifying new gene defects on a daily basis. This review will focus on primary genetic mitochondrial diseases that impair energy production and affect the nervous system, pathophysiology of disease, classical phenotypes, diagnosis, and treatment.