The association between apolipoprotein E (apoE) genetic polymorphism and stroke has not been concordant in different racial populations. We investigated the association between apoE genotypes and stroke subtypes by a case-control study in Bangladesh for the first time among south Asian countries. First-ever-stroke patients (n=227; cerebral infarction, n=147, cerebral hemorrhage, n=80) and 190 controls were recruited from a hospital in Dhaka, Bangladesh. The diagnosis of stroke was based on CT and clinical findings. Cerebral infarction was classified anatomically into cortical and penetrating region. Infarction in the cortical region was further categorized etiologically into thrombosis and embolism. Cerebral hemorrhage was considered as a whole in all analyses. ApoE genotypes were determined by restriction fragment length polymorphism. In the multivariate conditional logistic regression analysis adjusted for potential confounders both the epsilon3/epsilon4 genotype and epsilon4 carrier conferred an approximately 3-fold increased risk for cerebral thrombosis in the cortical artery region (OR 3.5, 95% CI 1.2 to 10.4 and OR 3.1, 95% Cl 1.1 to 9.0, respectively) compared with epsilon3/epsilon3 genotype. However, when the analysis was restricted to the elderly (>60 years), epsilon 2 carrier was associated with a risk of hemorrhagic stroke (OR 19.2, 95% CI 1.3 to 295.2). Our study suggested that both apoE epsilon3/epsilon4 genotype and epsilon4 carriers were risk factors for cerebral thrombosis in cortical artery region, whereas epsilon 2 carrier was a risk factor for hemorrhagic stroke in the elderly.