To describe fetal and neonatal mortality due to congenital anomalies in Colombia.We analyzed all fetal and neonatal deaths due to a congenital anomaly registered with the Colombian vital statistics system during 1999-2008.The registry included 213,293 fetal deaths and 7,216,727 live births. Of the live births, 77,738 (1.08%) resulted in neonatal deaths. Congenital anomalies were responsible for 7321 fetal deaths (3.4% of all fetal deaths) and 15,040 neonatal deaths (19.3% of all neonatal deaths). The fetal mortality rate due to congenital anomalies was 9.9 per 10,000 live births and fetal deaths; the neonatal mortality rate due to congenital anomalies was 20.8 per 10,000 live births. Mortality rates due to congenital anomalies remained relatively stable during the study period. The most frequent fatal congenital anomalies were congenital heart defects (32.0%), central nervous system anomalies (15.8%), and chromosomal anomalies (8.0%). Risk factors for fetal and neonatal death included: male or undetermined sex, living in villages or rural areas, mother's age >35 years, low and very low birthweight, and <28 weeks gestation at birth.Congenital anomalies are an important cause of fetal and neonatal deaths in Colombia, but many of the anomalies may be preventable or treatable.