The indigenous Austronesian minority of Taiwan is heavily affected by health disparities which may include suffering from a greater burden of the tobacco epidemic. While a lack of representative data has historically precluded an investigation of the differences in smoking between Taiwanese ethnicities, these data have recently become available through an annual population-based telephone survey conducted by the Health Promotion Administration, Ministry of Health and Welfare (previously known as the Bureau of Health Promotion (BHP), Department of Health). We used the BHP monitoring data to observe the prevalence of smoking and environmental tobacco smoke exposure among indigenous and non-indigenous Taiwanese surrounding a tobacco welfare tax increase in 2006, investigate ethnic differences in smoking prevalence and environmental tobacco smoke exposure each year between 2005 and 2008, and perform multiple logistic regression to estimate measures of association between potential risk factors and smoking status. Despite significant ethnic and gender differences in smoking prevalence, smoking status was not found to be significantly associated with ethnicity after controlling for socioeconomic and demographic factors.