Background: Numerous studies have evaluated the association between the apolipoprotein E (apoE) gene polymorphisms in coronary heart disease (CHD). However, the results remain uncertain. We carried out a meta-analysis to derive a more comprehensive estimation of the association in Chinese population. Methods: Case-control studies in Chinese and English publications were identified by searching databases of PubMed, EMBASE, Web of Science, CNKI, CBM, Wanfang, VIP and hand searching of relevant journals and the reference lists of retrieved articles. Odds ratio (OR) and 95% confidence interval (CI) were applied to assess the strength of the associations. Subgroup analysis and sensitivity analysis were performed to explore the between-study heterogeneity. Results: We finally identified 61 relevant studies which comprised 6634 case-patients and 6393 controls. The pooled OR for epsilon 4 carriers was 96% higher than the epsilon 3/3 genotype for CHD (OR, 1.96; 95% CI, 1.70 to 2.24; P< 0.001). However, there was no evidence of statistically significant association between epsilon 2 carriers and risk of CHD (OR, 1.02; 95% CI, 0.91 to 1.13; P = 0.729). In the subgroup analysis, different endpoints may partially account for the heterogeneity. No publication bias was found. Conclusions: Our meta-analysis suggests that the apoE epsilon 4 allele may be a risk factor for CHD in the Chinese population, however, epsilon 2 allele has no significant association.