Aim To evaluate the apolipoprotein E (Apo E) genotype distribution in two type of stroke. Methods Polymerase chain reaction restriction segment length polymorphism (PCR RFLP) wae used to examined the Apo E genotype in 180 patients with hemorrhagic stroke (90) and ischemic stroke (90), along with the 107 age and sex matched controls. Results The frequency of Apo E ε2/ε3 was higher in hemorrhagic stroke group (28.9%) than in the controls (16.7%, P<0.05), while the Apo E ε3/ε3 frequency was lower in the cases (54.4%) than in the controls (70.0%, P<0.05). The Apo E ε3/ε4 was more frequent in the ischemic stroke group (21. 1%) than in the controls (8.9%, P<0.05). Conclusion Apo E ε2 may be related to the risk of hemorrhagic stroke and that Apo E ε4 may be an important risk factor for ischemic stroke.