Objectives: Studies on the geographical differences in mortality tend to use a census population, rather than a registration population, as the denominator of mortality rates in South Korea. However, an administratively determined registration population would be the logical denominator, as the geographical areas for death certificates (numerator) have been determined by the administratively registered residence of the deceased, rather than the actual residence at the time of death. The purpose of this study was to examine the differences in the total number of a district population, and the associated district-specific mortality indicators, when two different measures as a population denominator (census and registration) were used. Methods: Population denominators were obtained from census and registration population data, and the numbers of deaths (numerators) were calculated from raw death certificate data. Sex- and 5-year age-specific numbers for the populations and deaths were used to compute sex- and age-standardized mortality rates (by direct standardization methods) and standardized mortality ratios (by indirect standardization methods). Bland-Altman tests were used to compare district populations and district-specific mortality indicators according to the two different population denominators. Results : In 1995, 9 of 232 (3.9%) districts were not included in the 95% confidence interval (CI) of the population differences. A total of 8 (3.4%) among 234 districts had large differences between their census and registration populations in 2000, which exceeded the 95% CI of the population differences. Most districts (13 of 17) exceeding the 95% CI were rural. The results of the sex- and age-standardized mortality rates showed 15 (6.5%) and 16 (6.8%) districts in 1995 and 2000, respectively, were not included in the 95% CI of the differences in their rates. In addition, the differences in the standardized mortality ratios using the two different population denominators were significantly greater among 14 districts in 1995 and 11 districts in 2002 than the 95% CI. Geographical variations in the mortality indicators, using a registration population, were greater than when using a census population. Conclusion: The use of census population denominators may provide biased geographical mortality indicators. The geographical mortality rates when using registration population denominators are logical, but do not necessarily represent the exact mortality rate of a certain district. The removal of districts with large differences between their census and registration populations or associated mortality indicators should be considered to monitor geographical mortality rates in South Korea.