Objectives: To explore the difference between the datasets of the death registration of the Department of Health (DOH) and Ministry of Interior (MOI) for the reference of the researchers in the future. Methods: We used the annual number of deaths published by the MOI and DOH during 1982-2002 to analysis the difference; and linking the datasets of the death registration of MOI and DOH, published in 1999, by ID number to verify the actual difference in the number of cases. Results: The concordant rate of number of deaths published by DOH and MOI was 98.7%. When the datasets were linked by ID number, the concordant rate was dropped to from 98.7% to 95.9%. There were 6,203 cases from the MOI dataset and 4,747 cases from the DOH dataset not matched by ID number. The rate of mismatch varied by age and area. Conclusions: The difference in the number of death published by DOH and MOI was about 2%. When the datasets were linked by each ID number, the difference in the number of death was increased to 4%. The concordant rate between the datasets of DOH and MOI varied by age and area. When using the dataset of death registration from the DOH or MOI for study, researchers should be aware of the variance. The causes of the difference and policy implication of this should be investigated in further study.