Background: Metabolic disorders, including obesity, are often accompanied by an increased risk of cardiovascular complications. Monocytes are the common link between obesity and cardiovascular diseases (CVDs). The bias of innate cellular immunity towards pro-inflammatory activation stimulates the development of diseases associated with chronic inflammation, in particular metabolic disorders, including obesity, as well as CVDs. Disorders in the functional state of monocytes and activation of inflammation may be associated with mitochondrial dysfunction. Mutations accumulating in mitochondrial DNA with age may lead to mitochondrial dysfunction and may be considered a potential marker for developing chronic inflammatory diseases. Methods: The present study aimed to study the relationship between mitochondrial heteroplasmy in CD14{}^{+} monocytes and cardiovascular risk factors in 22 patients with obesity and coronary heart disease (CHD) by comparing them to 22 healthy subjects. Results: It was found that single-nucleotide variations (SNV) A11467G have a negative correlation with total cholesterol (r = –0.82, p 0.05), low density lipoproteins (LDL) (r = –0.82, p 0.05), with age (r = –0.57, p 0.05) and with mean carotid intima-media thickness (cIMT) (r = –0.43, p 0.05) and a positive correlation with HDL level (r = 0.71, p 0.05). SNV 576insC positively correlated with body mass index (BMI) (r = 0.60, p 0.001) and LDL level (r = 0.43, p 0.05). SNV A1811G positively correlated with mean cIMT (r = 0.60, p 0.05). Conclusions: It was revealed that some variants of mitochondrial DNA (mtDNA) heteroplasmy are associated with CVD risk factors. The results demonstrate the potential for using these molecular genetic markers to develop personalized CVD and metabolic disorder treatments.