It has been reported that three common loci, SstI, C-482T, and T-455C, in the apolipoprotein C3 (APOC3) gene might be associated with an increased risk of coronary heart disease (CHD). Considering the inconsistent results and ethnicity variations, we performed a systematic meta-analysis to evaluate the association between three single nucleotide polymorphisms (SNPs) and the risk of CHD.We searched HuGE Navigator and PubMed databases to screen for the related literature published before 25 September, 2015. Two independent reviewers extracted the data and assessed the study quality. A random-effect model was used to pool the effect size.A total of 29 studies met inclusion criteria. Nineteen studies, including 11,186 subjects relative to SstI, five studies comprising 3727 subjects relative to C-482T, and nine studies with 6753 subjects relative to T-455C were included in the final analysis. A significant increase in CHD risk was observed in the SstI polymorphism (S2 versus S1: odds ratio [OR] = 1.30, 95% confidence interval [CI] 1.10-1.55. There was also a significant increasing trend of CHD risk in the T-455C polymorphism (C versus T: OR = 1.28, 95% CI 1.16-1.41. However, no associations between C-482T and CHD risk were found in this meta-analysis.The pooled evidence suggests that two SNPs (SstI and T-455C) are associated with an increased risk of CHD. However, because of the limited sample size and heterogeneity, further large-scale and well-designed studies are needed to validate our findings.