Objective To investigate the relationship of polymorphisms of CYP1A2 and CYP2C19 with prognosis of stable coronary heart disease in elderly patients receiving primary or secondary prevention. Methods A total of 241 men aged ≥ 60 years were enrolled, who was on long-term oral clopidogrel and received their annual health examination in Chinese PLA General Hospital between April and July 2017. The patients were divided, based on diagnosis of coronary heart disease, into primary prevention group (n=123) and secondary prevention group (n=118). For all patients, blood samples were collected on admission, platelet aggregation was measured, polymorphisms of CYP1A2 and CYP2C19 were assayed, and major adverse cardiovascular and cerebrovascular events (MACCE) were recorded during the follow-up as of before April 2019. The data were processed by SPSS statistics 23.0. t test and Pearson chi-square test were performed to compare the data between groups, and multivariate Cox proportional hazard model was used to compare the outcomes. Results According to polymorphisms of CYP1A2 and CYP2C19, all patients were divided into fast metabolism group and medium/slow metabolism group, and platelet aggregations induced by ADP and AA of the two groups were not significantly different (P>0.05). Multivariate Cox survival analysis showed that only age [hazard ratio (HR)=1.074,95% confidence interval (CI):1.003-1.150] was independent risk factor in primary prevention group, and that, after adjusting for baseline characteristics, age (HR=1.036,95%CI:1.000-1.075) and diabetes (HR=1.990,95%CI:071-3.696) were independent risk factors in secondary prevention group. However, the phenotypes of CYP2C19 and CYP1A2 had no effects on the prognosis (P>0.05). Conclusions The phenotypes of CYP1A2 and CYP2C19 had no significant effect on the platelet aggregation function and the risk of MACCE in the elderly patients receiving primary or secondary prevention with stable coronary heart disease.