Abstract There are strong evidences that common mitochondrial DNA (mtDNA) haplogroups may influence the pathogenesis of cardiovascular diseases (CVDs). In this matched case-control study, we investigate the association between mtDNA haplogroups and two CVDs, myocardial infarction (MI) and stroke, and classical cardiovascular risk factors. Data obtained show that haplogroup H constitute a susceptibility risk factor for MI (p = 0.001; OR = 2.379, 95% CI [1.440–3.990]). Otherwise, our data also suggest a beneficial role of haplogroup J against hypertension (p = 0.019; OR = 0.348, 95% CI [0.144–0.840]). These results may provide some guidance for predicting the genetic risk of these diseases in different human populations through the differences in energy efficiency between haplogroups. Highlights • Mitochondrial haplogroup H constitutes a susceptibility factor for MI and J provides a beneficial role against hypertension. • Common mitochondrial DNA (mtDNA) haplogroups might influence the pathogenesis of cardiovascular diseases. • Investigated the association between mtDNA haplogroups in myocardial infarction, stroke, and cardiovascular risk factors. • Haplogroup H constitutes a susceptibility factor for MI. • Haplogroup J provides a beneficial role against hypertension. [ABSTRACT FROM AUTHOR]