At the Instituto Materno Infantil (IMI) in Bogotá (Colombia), 5,686 births (5,597 live births and 89 stillbirths) were analyzed during two periods: from October, 1997, to April, 1998, and from July to November, 2000 (12 months). Congenital anomalies were detected in 4.4% of live newborn babies and in 7.8% of stillbirths. Major anomalies corresponded to 69% and mild anomalies to 31% (3% and 1.4% of all live births, respectively). The newborn babies with major anomalies, in comparison to the normal controls, had higher mortality at hospital discharge (p = 0.0001), lower average birth weight (p = 0.003), and family history of congenital anomalies (p = 0.0001). The only significant association for mild anomalies was with family history of congenital anomalies (p = 0.0001). The frequency of congenital anomalies was similar to that in other studies, although certain kinds of anomalies showed noticeable frequency differences. This may be a consequence of differences in record keeping or in detection methods.