Objective To investigate ATP-binding cassette transporter 1(ABCA1) M233V and R219K gene polymorphism in Mongolian nationality population in Inner Mongolia region and its correlationship with blood lipids and coronary heart disease(CHD). Methods The target fragments of ABCA1gene were amplified and analyzed by polymerase chain reaction-restriction fragments length polymorphism(PCR-RFLP) technique in 115 Mongolian control subjects without CHD and patients with CHD. Results The subjects presented ABCA1 gene M233V polymorphism, which had three genotypes: MM genotype, MV genotype and VV genotype. There was no significant difference in frequency of allele and genotype in M233V polymorphism between controls and CHD patients(P＞0.05). No significant difference was found in levels of total cholesterol(TC), triglyceride(TG), high density lipoprotein-cholesterol(HDL-C) and low density lipoprotein-cholesterol(LDL-C) between MM genotype and MV+VV genotype(P＞0.05).The frequency of KK genotype was significantly higher in controls than in CHD patients(P＜0.05). KK genotype had higher HDL-C level(P＜0.05) and lower TG level than RR genotype (P＜0.05).Conclusion In Mongolian population in Inner Mongolia region, M233V is a novel polymorphism in ABCAl gene. ABCAl gene R219K polymorphism is associated with CHD risk．The KK genotype results in a beneficial profile of blood lipids, which may be a novel genetic marker for low risk of CHD.