Background and Aim: Congenital anomalies are a worldwide problem, causing perinatal and infant deaths and postnatal physical disabilities. The present study was planned to highlight the pattern of congenital anomalies and its incidence, in new-borns. This study also included the assessment of various risk factors during antenatal and intranatal period, and their association with occurrence of congenital malformations in newborn babies, so that some preventive measures could be formulated. Material and Methods: A cross-sectional study was conducted at neonatal intensive care unit (NICU) of Medical College and Hospital, tertiary care institute of India. The study period was for the duration of 1 year. All the new born babies were thoroughly examined for the presence of congenital malformations. Detailed maternal history was recorded so as to evaluate association of various maternal risk factors with the congenital malformations. Results: During the study period, congenital malformations were detected in 120 new born babies. Out of this, 110 (91.6%) new born babies were live births and 10 (8.33%) were Intrauterine deaths. Most of the deliveries were full term 64 (53.3%) and only 56 (46.6%) were pre term delivered between 32 to 36 weeks of gestation. Among maternal and fetal risk factors; parental consanguinity, maternal under nutrition/obesity, positive history of a congenital anomaly (CA) in the family, and still birth/intrauterine deaths and ambiguous sex of the newborn baby were significantly associated with higher frequency of CAs (p<0.05). Conclusion: Congenital anomalies in this study were significantly associated with having inadequate antenatal care. With adequate antenatal care, pregnant women are often provided with health education on various issues such as the importance of proper nutrition, how to avoid teratogens, and prevention of maternal infections.