Aim To explore the relationship between carotid artery intima media thickness(IMT) and apolipoprotein E(apoE) genotypes among patients with premature coronary heart disease(CHD). Methods Eight five patients with documented premature CHD were recruited to participate in this study. The carotid artery IMT was checked by ultrasound imaging and apoE genotype was classified with the method of polymerase chain reaction restriction refraction length peptide. The relationship between carotid artery IMT and lipid parameters and apoE genotype were discussed. Results There were five kinds of apo egenotypes. Three main genotype according to the frequency were apoE3/3>apoE3/4>apoE₂/3 and apoE₂/4, and apoE4/4 were rare genotype. The allele of apoE also had different frequencies, ε3>ε4>ε2. Levels of serum TC and LDLC were higher in patients with apoE3/4 genotype than those with apoE₂/3 genotype, in verse to HDLC (p<0.05). There were higher values of IMT in apoE3/4 group than that in apoE₂/3. There was positive correlation between IMT and TC(r=0.401,p<0.01) and LDLC(r=0.376,p<0.01). Conclusions ApoE genotype influence carotid artery IMT at least partly through its lipid effect.