Objectives: Hualien county includes three aboriginal areas and can be used as a good example to illustrate the health differences between aboriginal and non-aboriginal regions. The aim of this study is to demonstrate the mortality trends between these two populations in their respective regions in Hualien from 1986 to 2005, and to compare the mortality rate before and after the launching of national health insurance in 1995. Methods: Mortality data comes from the Mortality Registry conducted by the Department of Health, from 1986 to 2005. Census data are based on the Taiwan-Fukein Demographic Fact Book from the Ministry of the Interior. We used the 5-year demographic distribution of Hualien in 2000 as the standardized population to calculate the direct standardized mortality rate. Results: The mortality rate in aboriginal areas decreased from 1575 (per 100,000) in 1986 to 1509 in 2005. The same trend was also evident in the non-aboriginal area (1054 persons/per 100,000 in 1986 to 765 in 2005). But the relative ratio of the mortality rate between aboriginal and non-aboriginal regions rose from 1.49 in 1986 to 1.97 in 2005. The mortality rates due to accidents, cirrhosis of the liver, and tuberculosis declined, but aboriginal areas still had a higher rate than the non-aboriginal area. Conclusions: The overall mortality rate in Hualien decreased from 1986 to 2005, irrespective of whether a region was classified as aboriginal or non-aboriginal. But the mortality trends between the two populations in their respective regions were significantly different. An increasing health disparity was evident in this study during the study period. This indicates that additional studies to determine the risk factors that affect health in aboriginal areas are needed in the future.