There are two major ethnic categories in Taiwan, i.e., the Han Chinese (98%) and the Taiwanese Aborigines (2%). The interethnic disparities in ischemic stroke etiological subtypes, conventional and behavioral vascular risk factors were unknown.From June 2007 to May 2009, a prospective stroke registry was conducted by a referral hospital in Taitung, Taiwan. Using the database, the interethnic disparities were examined by univariate analyses, followed by multivariate analysis of the ischemic stroke subtype [by TOAST (Trial of Org 10172 in Acute Stroke Treatment) classification] with significant difference between the two ethnicities.We included 433 acute ischemic stroke patients, comprising 302 Han Chinese (70%) and 131 Aborigines (30%). The Taiwanese Aborigines are more likely to be illiterate and living in rural areas (both p < 0.001); they are also more likely to have atrial fibrillation (p = 0.018), and to engage in alcohol drinking (p = 0.046) and areca nut chewing (p < 0.001), but less likely to have diabetes mellitus (p = 0.022). Univariate analysis shows higher prevalence of cardioembolism among the Taiwanese Aborigines. However, ethnicity is not one of the independent variables of cardioembolism, which include atrial fibrillation [odds ratio (OR) = 28.04; 95% confidence interval (CI), 13.39–58.72)], hyperlipidemia (OR = 0.46; 95% CI, 0.23–0.95), and areca nut chewing (OR = 2.85; 95% CI, 1.21–6.72).Risk factors differ between the Han Chinese and the Taiwanese Aborigines, and areca nut chewing correlates with cardioembolic stroke. Future measures for stroke prevention should take these factors into consideration.