Background: To study the system-wise occurrence of congenital anomalies in newborns admitted in a tertiary hospital and to study the associated maternal factors.Methods: This is a retrospective study of all the mothers and their newborn babies with congenital anomalies who were delivered or referred to the Obstetrical Department / Neonatology unit during a two-year study period. The maternal risk factors and associated Obstetric complications were studied.Results: Among the babies born with congenital anomalies, the systems most involved were Genito-urinary System (28.5%) and Cardiovascular System (20.5%). Among the maternal risk factors, Diabetes (14.01%), previous abortions (12.7%) and hypothyroidism (8.7%) were the most significant associated factors. Intrauterine growth restriction (17.4%) was noted to be more common in these babies.Conclusions: The incidence of anomalies was most involving the Genito-urinary System and Cardiovascular System. The major risk factor identified was maternal Diabetes. Prevention by public awareness during adolescence, pre-conceptional counseling and antenatal screening is stressed. Availability of Pediatric surgery and Rehabilitative facilities to improve the quality of life would be warranted.