The circadian rhythm regulates various physiological mechanisms, and its disruption can promote many disorders. Disturbance of endogenous circadian rhythms enhances the chance of myocardial infarction (MI), showing that circadian clock genes could have a crucial function in the onset of the disease. This case-control study was performed on 1057 participants. It was hypothesized that the polymorphisms of one nucleotide (SNP) in three circadian clock genes (CLOCK, ARNTL, and PER2) could be associated with MI. Statistically significant differences, estimated by the Chi-square test, were found in the distribution of alleles and genotypes between MI and no-MI groups of the CLOCK (rs6811520 and rs13124436) and ARNTL (rs3789327 and rs12363415) genes. According to the results of the present study, the polymorphisms in the CLOCK and ARNTL genes could be related to MI.