We performed an association analysis for the mtDNA major common variants and haplogroups with incidence of myocardial infarction and essential prognostic characteristics in patients. A comparison of patients (N = 406) and control groups (N = 183) uncovered a higher frequency of HV0 haplogroup in patients (6.9% vs. 2.2%; p = 0.033). Patients with early infarction (before age of 55 in men) had a higher frequency of 16189C variant, compared to patients who endured first infarction at age older than 55 (24.1% vs. 12.5%; p = 0.008). In addition, haplogroup U2e was only detected in the subgroup with early infarction (4.4%; p = 0.004). Haplogroup U5 was less frequent in patients with early infarction (5.1% vs. 15.4%; p = 0.002). Observations during a 1-year follow-up uncovered that patients with recurring cardiovascular incidents had higher frequency of haplogroup H1 (20%, versus 4.5% in patients without complications, p = 0.002) and variant 16189C (30% versus 13.5%; p = 0.018). Haplogroup U5 was more frequent in the subgroup of patients with lower (<40%) ventricular ejection fraction (17.1%, compared to 8.2%; p = 0.034). Thus, our results indicate that mtDNA polymorphism contributes to coronary atherosclerosis. The obtained associations can be explained by the effect of polymorphisms on oxidative phosphorylation and the production of reactive oxygen species in mitochondria.