We analyzed the AluI restriction fragment length polymorphism (RFLP) of the apolipoprotein B (apoB) gene to determine the association between AluI allelic distribution and the occurrence of ischemic stroke in Taiwan. A total of 44 healthy volunteers and 159 ischemic stroke patients were included in the study. The allele frequency of AluI was very similar in the two groups, 0.87 in the patient group and 0.89 in the control group, for the major allele A-. The distribution of A-/A-, A-/A+, and A+/A+ genotypes of the patients was not significantly different from that of the controls. Among ischemic stroke patients, the A+ allele of the AluI restriction site was significantly associated with elevated apoB levels. The results of this study suggest that the presence of the rare AluI RFLP may contribute to an elevated plasma apoB level, which is a known risk factor for ischemic stroke.