To study the relative frequency of apoE allele and the influence of polymorphism on serum lipid and lipoprotein concentration in Uygur nationalities, apoE phenotype was analysed by polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) in 163 Uygurs and 150 Hans. Serum lipid levels were measured in 101 Uygurs and 140 Hans of them. The results showed that the frequency of E4 allele was higher in the Uygurs than in the Hans. Total cholesterol and low-density lipoprotein cholesterol were higher in the two nationalities who bear E 4 allele. It is concluded that the distribution of apoE genotypes and allele-frequencies was significantly different, but the trent for the relationship between apoE phenotype and lipid and lipoproteins was similar in the two nationalities.