Atherosclerosis, the primary cause of cardiovascular disease, is a complex and multifactorial pathology resulted from the harmful interactions between genetic and environmental factors. There is a growing body of evidence in support of the role of mitochondrial factors in the pathogenesis of atherosclerosis. Impaired mitochondrial function and structural and qualitative changes in mitochondrial components such as mitochondrial DNA (mtDNA) damage may be directly involved in the development of multiple mechanisms of atherogenesis. Recent findings show that several heteroplasmic mutations of mtDNA are related to atherosclerosis, coronary heart disease and several atherosclerosis-related diseases such as arterial hypertension and diabetes mellitus. Therefore, heteroplasmic mtDNA mutations could represent a promising molecular biomarker of genetic susceptibility to atherosclerosis and related pathologies. This review is focused on the latest findings in the studies of mutations of mitochondrial genome, which are associated with atherosclerosis and atherosclerosis- related diseases.