Introduction: Congenital anomalies figure as fifth largest cause of neonatal mortality in India. Their pattern and frequency differs in different parts of world and hence prevalence studies need to be done. Material and Methods: A prospective hospital–based study was conducted at maternity and child health hospital Anantnag from June 2017 to May 2018. All neonates born with congenital anomalies were included in the study and complete maternal data and clinical examination supplemented with radiological or sonographic studies was done. Data was analysed in Microsoft excel and expressed as frequencies and percentages. Results: Out of total 65 babies with CA around 56% were males; 43% were preterm, 61% were low birth weight. 60% babies were born by consanguinity. There was bimodal age of distribution in mothers; in less than 20 yrs (30%), and greater than 30 years (46%). Congenital heart disease (21%) and central nervous system anomalies (20%) followed by musculoskeltal anomalies (15%) were the commonest anomalies encountered. Conclusion: The pattern of congenital anomalies is similar to other parts of northern India. Prenatal diagnosis and preventive measures like folic acid supplementation can pave a long way in prevention of a sizable fraction of congenital anomalies at least of neural tube defects.