Early diagnosis, before manifestation of symptoms or identifying susceptibility to diseases can reduce the severity and prevalence and may even control or inhibit the disease progression. Now the relationship between the incidence of cardiovascular diseases and certain types of haplotypes of human mtDNA (mitochondrial DNA) have been substantiated and investigation of the frequency of particular types of cases and controls can reveal this connection. Substitution of T to C at nucleotide position 16189 in the hypervariable D-loop of the control region (CR) of mitochondrial DNA (mtDNA) has attracted research interest because of its suspected association with various multifactorial diseases. The objective of the current study was to identify and evaluate different haplotype mtDNA and examine their relationship to the incidence of coronary artery disease in different haplogroups in Iranian patients visiting SINA hospital in Tehran. A total of 70 participants (including 40 males and 30 females) visiting the Cath Lab (angiography) of SINA hospital were selected according to the index of stenosis (CSI). After obtaining informed consent, approximately 5cc of blood sample from each patient was taken and sent to the laboratory. Total DNA (50 μg) of blood samples were extracted using primers of D-Loop- a specific region of mtDNA, the replicative samples (HVS regions) were then seperated by electrophoresis process and quality of amplicon (product) was confirmed. This step was followed by sequencing and compared with the reference sequence. According to the SNP, polymorphisms and mutations, and the percentage of their presence in case and control populations were studied and the data analyzed. Items have been composed of haplotype 263 A>G (maximum) with 62 samples from 34 patients and 23 healthy and 5 mild cases, 310-311 insC with 61 samples from 35 patients, 21 healthy and 5 slight, variant 750 A>G with 59 persons of 33 patients, 20 healthy and 6 average, other SNP 73 A>G with 45 samples from 23 patients, 17 healthy and 5 average, 40 varieties of 16519 T>C with 24 patients, 13 healthy and 3 middle and 32 of the 309-310 ins C with 17 patients, 10 healthy and 5 are mild cases. Some changes, such as C>T and insCC, regardless of position, as well as history and ethnic studies were evaluated. The 263 A>G, 310-311 insC, 750 A>G, 73 A>G, 16519 T>C and 309-310 insC with high frequency are more important in patients with cardiovascular disorders. These changes (except 750 A>G and sex variable) have been previously established with certain diseases, however in the present study no particular allelic association were revealed. In this study susceptibility of men against women is 6.6 times and 750 A>G significantly increases 1.6 times the risk of CAD.