Background: Congenital malformations are any irreversible condition existing in a child before birth, can be structural or functional anomalies and can be identified before birth, at birth or sometimes in later childhood. Aim: This study was carried out with aim to determine the incidence, pattern, various risk factors and outcome of congenital anomalies in neonates born in a tertiary care hospital and also emphasis the need of early detection and intervention, for decreasing associated morbidity and mortality. Early detection may give a chance to decide upon continuation of pregnancy and encourage preventive measures for prevention of its recurrence in subsequent pregnancy. Methods: This was an observational prospective study carried out in a tertiary care hospital in western Maharashtra, to study about the pattern of congenital malformation in this region. Data was analyzed using SPSS version 20. Results were presented in the tabular form and numbers of variables presented with help of frequency and percentages. Results: During the study period, 17000 babies were born, of which 300 had congenital malformations, making the incidence 17.6 per 1000 births of which 56% were male and 75% were less than 2.5kg. 46.7% babies were born to mothers >30yrs age. Out of the 300 cases, 20% died. The predominant system involved was central nervous system (31%). Conclusion: In India, prevalence of congenital anomalies remains high, third most common cause of perinatal mortality, hence emphasis should be given to early detection and intervention. Also increased awareness about preventable risk factors may help in reducing the burden of congenital anomalies on perinatal morbidity and mortality and improve the outcome. Preventive and interventional strategies will reduce the incidence of birth defects, decrease burden and also improve quality of living.