Coronary artery disease (CAD) is suspected as a leading cause of mortality in developed countries. Due to cholesterol and fat deposit plaque is forming into the inner walls of the arteries of the heart, which leads to narrowing of blood vessels of heart and reduce the blood flow rate into heart. Proprotein convertase subtilisin-like kexin type 9 (PCSK9) is one of the candidate gene that regulate lipoprotein retention pathway of CAD development. It is a newly discovered serine protease that plays a key role in LDL-C homeostasis by mediating LDL receptor (LDLR). The LDL receptor is breakdown through a post transcriptional mechanism and induces the production of very low-density lipoprotein in the fasting state. The aim of this study was to investigate the frequency of single nucleotide polymorphism (SNP) of PCSK9 gene of 155 CAD patients and 102 ages matched healthy controls. Serum lipids including total cholesterol (TC), triglycerides (TG), HDL, LDL, and VLDL were analyzed. PCR-RFLP analysis was carried out to genotype regions carrying Eam 1104I restriction site in the PCSK9. Gene considering significant difference in serum TC, TG, HDL-C, LDL-C and VLDL-C levels (P<0.001, <0.0001) of patients and control samples. In CAD patients, G allele frequency is less than A allele frequency. G allele is responsible for decreasing the LDL: HDL ratio which shows evidence in having its protecting effect on the occurrence of CAD in West Bengal Population.