We investigated the livebirths prevalence and occurrence pattern of birth defects in Korea. After the survey on birth defects was done in 2,348 medical institutions around the nation, the birth defect prevalence of livebirths in 2005-2006 was calculated. This study was based on the medical insurance claims database of the National Health Insurance Corporation. The number of livebirths in Korea was 883,184 from 2005-2006, and 25,335 cases of birth defects were notified to our study, equivalent to a prevalence of 286.9 per 10,000 livebirths. Anomalies of the circulatory system were the most common defects, accounting for 43.4% of birth defects with a prevalence of 124.5 per 10,000 livebirths. It was followed by the musculoskeletal system anomalies, the digestive system anomalies, and the urinary system anomalies. The five major birth defects based on the ranking of prevalence were atrial septal defect, ventricular septal defect, hydronephrosis, patent ductus arteriosus, and cleft lip/palate. Birth defects in livebirths were associated with a high proportion of low birthweight, prematurity, multiple births and advanced maternal age. The prevalence of birth defects in Korea is similar to or lower than those reported in developed countries. Our study suggests baseline data to explain the current status of birth defects and to establish a registry system of birth defects in Korea.