Background The association of vitamin D level and vitamin D receptor (VDR) gene polymorphisms with the prevalence of coronary artery disease (CAD) has been evaluated in various studies; however, the reported results were inconsistent. Hence, we aimed to investigate the impact of two VDR gene polymorphisms, TaqI (rs731236) and BsmI (rs1544410), on the incidence and severity of CAD in Iranian population. Methods Blood samples were collected from 118 CAD patients underwent elective percutaneous coronary intervention (PCI) and 52 control subjects. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was performed for genotyping. SYTNAX score (SS) was calculated as a grading tool for complexity of CAD by an interventional cardiologist. Results TaqI polymorphism of VDR was not associated with the incidence of CAD. A significant difference was observed between CAD patients and controls regarding BsmI polymorphism of VDR (p < 0.001). GA and AA genotypes was significantly associated with a decreased risk of CAD (p = 0.01, p-adjusted = 0.01 and p < 0.001, p-adjusted = 0.001 respectively). A allele of BsmI polymorphism was shown to have a protective effect against CAD (p < 0.001, p-adjusted = 0.002). No association was found between TaqI and BsmI polymorphisms of VDR and SS as a measure of CAD severity. Conclusion Association of BsmI genotypes with the incidence of CAD revealed that the genetic variation of VDR might play a role in the pathogenesis of CAD.