Mitochondrial dysfunction is associated with the hallmarks of cancer, aging, and age-related diseases. In recent years, numerous molecular mitochondrial alterationss have been identified at the DNA, RNA, and protein levels, as well as metabolic shifts and metabolic reprogramming in various types of cancer and age-related diseases. The review analyzes a number of clinically significant parameters of mitochondrial disorders, including susceptibility to disease development, diagnosis, prognosis, and the course of these pathologies. The manifestations of mitochondrial dysfunction at the molecular level are constantly being refined and revised, so in the future, we can expect the emergence of new clinically significant signs of these disorders in cancer and age-related diseases.