Objective <p>Many studies have shown that apolipoprotein E (ApoE) gene polymorphisms have an impact on coronary artery disease. However, the role of ApoE gene polymorphisms in secondary prevention is still unclear. The purpose of this study was to retrospectively investigate the influence of apolipoprotein E gene polymorphisms on the prognosis of coronary artery disease.</p> Methods <p>We collected and compared the clinical information of patients hospitalized for percutaneous coronary intervention (PCI). Multivariate hierarchical logistic regression was used to evaluate the relationship between ApoE gene polymorphisms and the prognosis of coronary artery disease in patients undergoing PCI.</p> Results <p>After statin treatment, the concentrations of triglycerides, LDL-C and total cholesterol significantly decreased in patients with ε3/ε4, ε3/ε3, ε2/ε3 and ε2/ε2 (<i>p</i> &lt; 0.05), whereas the concentrations of triglycerides, LDL-C and total cholesterol did not significantly decrease in patients with ε4/ε4 (<i>p</i> &gt; 0.05). After statin treatment, the incidence rates of hypertriglyceridemia, high LDL-C and high total cholesterol significantly decreased in patients with ε3/ε4, ε2/ε3 and ε3/ε3 (<i>p</i> &lt; 0.05), whereas the incidence rates of hypertriglyceridemia, high LDL-C and high total cholesterol did not decrease significantly in patients with ε4/ε4 (<i>p</i> &gt; 0.05). Multivariate logistic regression model suggested that there were no significant differences in the incidence rates of secondary PCI or in-stent restenosis in patients with different ApoE genotypes one year following PCI (<i>p</i> &gt; 0.05).</p> Conclusion <p>After secondary prevention, there was no significant difference in the incidence of in-stent restenosis or secondary PCI among patients with different ApoE genotypes one year after PCI.</p>