A number of case-control studies have been conducted to investigate the relationship between the ATP-binding cassette transporter A1 (ABCA1) gene polymorphisms and risk of coronary heart disease (CHD). However, the results have been inconclusive. The purpose of the present study is to investigate whether this polymorphism confers significant susceptibility to CHD using a meta-analysis. We conducted searches of the published literature in PubMed, Embase, and CBM databases. 13 studies were included in our meta-analysis, involving a total of 11,678 individuals. Subgroup analyses were performed by ethnicity and cancer type. Statistically significant association between ABCA1 gene R219K polymorphism and increased CHD risk was found in total population analyses in all four genetic comparison models (OR(C vs. T) 1.19, 95% CI 1.07-1.31; P = 0.001; OR(Homozygote model) 1.28, 95% CI 1.07-1.52; P = 0.007; OR(Recessive genetic model) 1.22, 95% CI 1.04-1.44, P = 0.015; OR(Dominant model) 1.21, 95% CI 1.07-1.35; P = 0.001). In subgroup analyses based on ethnicity, the association was still significant in Asians (All P values < 0.001), but not in Caucasians (All P values > 0.05). ABCA1 R219K polymorphism is associated with CHD susceptibility, and individuals with ABCA1 have a significantly higher risk of cancer particularly in Asians.