Coronary artery disease (CAD) is a major cause of mortality and morbidity around the whole world. The polymorphisms of Apolipoprotein A-I (Apo-A1), including rs670 (-75 G/A) and rs5069 (+83 C/T), have been found to be probably associated with the risk of CAD. However, the results were inconsistent. To determine the association between Apo-A1 rs670 and rs5069 polymorphisms with CAD, we conducted the meta-analysis of all available studies cited in Pubmed, Embase, CBM and CNKI before 11 Mar 2017. A total of 6 studies, including 1358 cases and 863 controls, were identified for the meta-analysis. The results showed that rs670 and rs5069 had no significant associations with risk of CAD in the overall analysis. But in subgroup analysis by ethnicity, the GG of rs670 was associated with a significantly lower risk of CAD in allelic model (OR = 0.61, 95% CI = 0.61 [0.38, 0.96], p = 0.03) and homozygous model (OR = 0.25, 95% CI = 0.25 [0.15, 0.44], p<0.00001) in Caucasians, the GG of rs670 was associated with a significantly higher risk of CAD in homozygous model (OR = 2.12, 95% CI = 2.12 [1.27, 3.53], p = 0.004) in Asian, and a lower risk of CAD for the CC genotype and C allele of rs5069 in allelic model (OR = 0.21, 95% CI = 0.21 [0.06, 0.72], p = 0.01) and homozygous model (OR = 0.11, 95% CI = 0.11 [0.04, 0.32], p<0.00001) in Caucasians. In conclusion, this study suggested that Apo-A1 rs670 and rs5069 had no significant associations with risk of CAD in the overall analysis. However, the results of this meta-analysis are hypothesis-generating results which should be interpreted with caution because of the heterogeneity and publication bias among study designs.