Apolipoprotein E plays a key role in the regulation of lipid metabolism. ApoE function is determined by the presence of three common alleles (epsilon2, epsilon3, epsilon4). The apo epsilon3 allele is the most prevalent, apo epsilon2 is associated with dysbetalipoproteinaemia, and apo epsilon4 is frequently associated with an increased risk for cardiovascular and Alzheimer's diseases. Mongolian population has a high rate of cardiovascular mortality and morbidity and there might be genetic susceptibility of the population to cardiovascular disease. The aim of our study was to establish the frequency of apoE genotypes in 744 Mongolian subjects and to compare the results with findings from other Asian populations. The apo E sequence was amplified using polymerase chain reaction and apo E genotyping was performed by restriction enzyme cleavage with CfoI. The relative apoE allele frequencies were epsilon2 = 3.7%, epsilon3 = 80.8%, and epsilon4 = 15.5%, the genotype frequencies were epsilon2/epsilon2 = 0% (N = 0), epsilon2/epsilon3 = 5.7% (N = 42), epsilon2/epsilon4 = 1.7% (N = 13), epsilon3/epsilon3 = 65.3% (N = 486), epsilon3/epsilon4 = 25.4% (N = 189), epsilon4/epsilon4 = 1.9% (N = 14); the occurrence of the risk epsilon4 allele in Mongolia is among the highest in Asia. The high frequency of the apo epsilon4 allele may increase the susceptibility of Mongolian population to cardiovascular diseases.