BACKGROUND: Apolipoproiein (Apo E) is one of the major proteins involved in catabolism of triglyceride (TG)-rich lipoproteins. Apo E poly-morphism contributes to the variation in plasma cholesterol levels and may influence the risk of atherosclerosis. This study was undertaken to know whether apo E polymorphism is associated with carotid artery intima, media thickness and plaque formation in type 2 diabetic patients. METHODS: We determined the apo E genotypes of 130 type 2 diabetic patients by modified Amplification Refractory Mutation System (ARMS) and classified all patients into E2, E3, E4 subgroups. The carotid artery IMT and plaque formation were determined with B-mode ultrasonography. RESULT: The apo E allele frequency of patients were E2 11.5%, E3 76.2%, FA 12.3% (p=0.0001). LDL-cholesterol levels were higher in patients with E4 allele, and HDL-cholesterol levels were lower in patients with FA allele than in patients with E2, E3 subgroups. The patients with carotid artery plaque have more E4 alleles in comparison to the patients without it(p=0.0001). FA allele group has higher carotid IMT than E2 and E3 allele groups (p=0.013). CONCLUSIONS: Apo E polymorphism is associated with carotid artery IMT and plaque formation in type 2 diabetic patients. Patients with E4 isoform is more likely to develop the atherosclerosis, carotid and coronary artery diseases than other apo E isoforms.