Early prevention of the development and timely diagnosis of cardiovascular system diseases are some of the main problems in modern cardiology. One promising approach is to identify relationships between carriage of mitochondrial DNA (mtDNA) mutations and development of cardiovascular diseases. Mitochondria are the only source of energy accumulation in cardiomyocytes; therefore, failure of their functioning caused by mtDNA mutations directly affects the bioenergetics and work of myocardial cells. The objective of this review is to describe the current achievements in studying the relationships of mutant mtDNA with the development of various cardiovascular system diseases.