Prospective case control study, carried out in a tertiary care hospital. The aim of present study was to find genetic markers for coronary artery disease (CAD) in north Indian population. Total number of 355 angiographically proven cases and 303 controls were included in the present study. Polymerase chain reaction- restriction fragment length polymorphism (PCR-RFLP) analysis was done for genotyping of ACE, MTHFR, Apo B Apo E. Significant association was observed for D allele of ACE (p=0.048, OR 1.27, 95% CI 0.99-1.62) and T allele of MTHFR (p=0.049, OR 1.45, 95% CI 0.98-2.13) with CAD. The mutant allele of Apo B (C7673T) was found significantly higher in controls than patients (p <0.001, OR 0.46 95% CI 0.33-0.65). However, an insignificant difference was observed for Apo E polymorphisms when E2 allele compared with E3 (p=0.15, OR 0.75 95% CI 0.49-1.14) and E4 allele compared with E3 (p=0.059, OR 1.58, 95% CI 0.96-2.61). The finding suggests that T allele of MTHFR gene and D allele of ACE gene is significantly contributed with CAD. Whereas, mutant allele of Apo B, E2 and E4 alleles are insignificantly associated with CAD. The study suggests that ACE and MTHFR gene may be as predictive molecular markers for CAD.