The review highlights current aspects of a large group of diseases the main pathogenetic element of which is an inherited or acquired disturbance of gene expression of nuclear or mitochondrial genome encoding mitochondrial proteins. The recent data on mutant genetic loci specific to the most wide spread mitochondrial diseases are considered. The steps of pathogenesis, include the mutations of nuclear or mitochondrial genes, disturbances of mitochondrial protein synthesis, dissipation of proton membrane potential, opening of a permeability transition pore, releasing of procaspases, cytochrome c, and other proapoptotic molecules, and finally chromatin fragmentation and apoptotic cell death. We discuss the possible reasons of polysymptomatic character and different variants of mitochondrial disease manifestations on the basis of the phenomenon of mitochondrial DNA heteroplasmy and metabolic compensation of the genetic defects. Modern biochemical methods of a mitochondrial disease diagnostics: (PCR-amplification, polarographic research of mitochondrial respiration and oxidative phosphorylation, analysis and monitoring of metabolites in biological liquids) are characterized. The basic principles and perspectives of the treatment of mitochondrial diseases, (gene therapy, correction of metabolic disorders, application of antioxidants and neuropeptides) are described.