Although genetic variants that affect susceptibility to coronary artery disease (CAD) have been greatly known, a number of these single nucleotide polymorphisms (SNPs) remain to be analyzed in populations with different ethnicities. CAD is influenced by numerous genetic, environmental, and lifestyle factors, and is an important reason for mortality around the globe. In this study, a novel SNP (rs6725887) in the WD Repeat Protein 12 (WDR12) gene was selected to be examined in Iranian patients with CAD. Ninety eigth healthy controls and one hundred and one CAD patients were enrolled from Iranian population, and their clinical data were collected for further comparisons. After DNA extraction from each sample, genotypes were characterized by Taq Man probe real- time PCR assay. Statistical analyses were performed to evaluate genotype and allele frequencies and compared the values with clinical variables. Body mass index, blood pressure, fasting blood sugar, LDL, HDL, cholesterol, and triglyceride significantly differed in CAD and control groups. Genotype and allele frequencies of rs6725887 in CAD patients and controls showed no significant association in the distribution. However, clinical parameters of CAD patients like HDL, LDL, FBS, TG, DBP and SBP had significantly (P<0.05) higher levels compared to control group. The rs6725887 polymorphism is unlikely to play a key role in CAD risk in our population. Further additional samples are required for better appreciation of the influence of WDR12 SNP on CAD occurrence.