We studied the relationship between apolipoprotein E gene polymorphism and persistent vegetative state (PVS) to explore the genetics background of PVS, and evaluated the effect of ApoE gene polymorphism on lipid levels in plasma. The ApoE genotype of fifty-six patients with PVS and fifty-three controls were determined by PCR and restriction fragment length polymorphism (PCR-RFLP). Plasma lipid levels were measured by using routine methods. Results demonstrated that there were five genotypes in the two groups: E3/3, E3/4, E2/2, E2/3 and E2/4. The genotype frequencies of ApoE gene in PVS were 21(37.5%), 26(46.4%), 2 (3.6%), 5(8.9%), 2(3.6%) and that in control were 37(69.8%), 7(13.2%), 2(3.8%) 5(9.4%), 2(3.8%) respectively. We compared the genotype frequencies between the two groups and found there was a significantly increase in E3/4(chi 2 = 14.236, P < 0.001) and decrease in E3/3(chi 2 = 5.348, P < 0.05). epsilon 2, epsilon 3 and epsilon 4 allele frequencies of ApoE were 11(9.8%), 73(65.2%), 28(25%) in PVS and were 11 (10.4%), 86(81.1%), 9(8.5%) in control respectively. Allele frequencies, significantly increased in epsilon 4 (chi 2 = 10.533, P < 0.001) and decreased in epsilon 3 (chi 2 = 7.022, P < 0.01). We also found that E3/4, E2/4 genotype and epsilon 4 allele can largely increase total cholesterol (TC) and lower density lipoprotein cholesterol (LDL-C) levels in plasma, and epsilon 2 alleles also can largely increase LDL-C levels inplasma. Our finding indicates that the ApoE gene polymorphism may be in association with the PVS, and may be a factor in the genetic susceptibility to PVS in Chinese; Genotype and alleles of ApoE in PVS can affect the lipid levels in plasma.