Background: In the present study, we estimated the population prevalence, associations of congenital heart defect (CHD) and mortality risk for DS using data from National Health Insurance Service (NHIS) and Rare Diseases Registry (RDR). Methods: We collected data on subjects with DS who were registered in the RDR between 2010 and 2015. To estimate associations of CHD and mortality risk of DS, the data of DS subjects were compared with 1:5 age-and sex-matched controls. Results: In 2015, 2077 individuals with DS were identified out of the total population of 51,574,044 South Koreans and the prevalence was 4.03 per 100,000 persons. The trend of DS population prevalence across 10-year-old intervals showed a peak in the group under the age of 10 years (26.0 per 100,000 persons) and then declined sharply after the age of 20 years (0.98 per 100,000 persons at 30-39 years of age). In subjects with DS, the frequencies of atrial septal defect [odds ratios (OR) =65.9; 95% CI, 84.1-99.1], ventricular septal defect (OR = 88.1, 95% CI, 57.9-134.1), patent ductus arteriosus (OR = 56.9, 95% CI, 40.1-80.8), tetralogy of fallot (OR = 42.1, 95% CI, 19.3-92.3), or atrioventricular septal defect (OR = 510.0, 95% CI, 126.7-999.0) were higher than those of age-and sex-matched controls. The risk of death in patients with DS was significantly higher than that of age-and sex-matched controls [hazard ratio (HR) =41.7, 95% CI 20.0-87.0]. Conclusion: In South Korea, the DS population prevalence was 4.03 per 100,000 persons in 2015. The subjects with DS were more likely to accompany CHD and have higher mortality risk than healthy controls.