To explore the distribution of polymorphisms of apolipoprotein E(apoE) gene and its relation to natural longevity in the Xinjiang Uighur people. Using polymerase chain reaction-restriction fragment length polymorphism(PCR-RFLP), the authors obtained data from centenarians(n=42), 90-year-old people (n=102), 65-70-year-old people (n=70) and controls(n=53). The frequencies of apoE genotypes epsilon 3/4, epsilon 3/3 and epsilon 2/3 were 2.4%, 69.0% and 23.8% respectively in the centenarian group, and the frequencies of their epsilon 4, epsilon 3 and epsilon 2 alleles were 1.2%, 82.1% and 16.7%. The frequencies of genotype epsilon 3/4 and epsilon 4, epsilon 3 allele in the centenarian group were significantly lower than those in controls(P< 0.01), whereas the frequencies of genotype epsilon 2/3 and epsilon 2 allele in the centenarian group were significantly higher than those in controls(P< 0.01). Longevity was noted to be positively correlated with epsilon 2 and negatively correlated with epsilon 4. This relationship reflects a genetic influence on differential survival and may point to pleiotropic age-dependent effects on longevity.