Abstract: Heteroplasmy mitochondrial DNA (mtDNA) markers and haplotypes of susceptibility or predisposition to atherosclerosis, coronary heart disease (CHD) and subdiagnosis of atherosclerosis and CHD and related medical conditions are disclosed. The biomarkers may be selected from the following heteroplasmy makers: 652lns/del G; A1555G; C3256T; T3336C; G12315A; G13513A; G14459A; G14846A; G15059A. Methods and kits for diagnosis, subdiagnosis, and prediction of clinical course and efficacy of treatments for CHD, atherosclerosis and related phenotypes using heteroplasmy in the risk genes and loci and other related biomarkers are thus provided. Novel methods for prevention and treatment of atherosclerosis, CHD and related conditions based on the disclosed CHD genes, loci, polypeptides and related pathways are also provided.