Aim To examine the distribution of R219K polymorphism of ATP binding cassette transporter 1(ABCA1) gene in Chinese population and to investigate the association of the SNP with lipid metabolism and the susceptibility to coronary atherosclerotic heart disease. Methods The target fragments of ATP binding cassette transporter 1 gene was amplified and analyzed by polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) technique in 133 unrelated normal control individuals and 49 familial hypercholesterolemia(FH) patients. The statistical analysis was implemented in statistical package SPSS. Results The observed allele frequencies were in accord with Hardy-Weinberg equilibrium. The frequency of ATP binding cassette transporter 1 219K allele was significantly higher in controls than that in FH patients (P=0.0001). Compared with the FH patients without 219K, the FH patients with 219K exhibited a significant decrease in plasma triglyceride concentration (1.14±0.55 mmol/L vs 1.76±0.58 mmol/L, P=0.001), and a trend of increase in plasma high density lipoprotein cholesterol concentration (1.39±0.54 mmol/L vs 1.21±0.32 mmol/L, P=0.061). Conclusions 219K polymorphism of ABCA1 gene was associated with higher high density lipoprotein cholesterol level and lower triglyceride level in FH patients and exert protective role for premature CHD in FH patients.