Introduction: Congenital malformations are defined as abnormalities of structures present at birth. The etiology of congenital malformations is heterogeneous. It can occur due to genetic, environmental and unknown causes. Various maternal risk factors are associated with its occurrence like advancing age, parity, socioeconomic status, previous history of malformations, maternal infections, chronic illness and nutritional diseases. Hence, this study is being conducted to see incidence of congenital malformations and its association with maternal risk factors. Material and Methods: A prospective observational study was conducted over a period of one year at a tertiary hospital. A total of 900 women were included in the study. A detailed obstetric history was taken. Women were followed up till deliveries. Data analysis was done by SPSS for windows version 2.0. Results: A Total of 900 deliveries were conducted, out of which there were 831 live births and 69 were stillbirths. Incidence of congenital malformations was found to be 68.89/1000 births (6.889%). Most common congenital malformation seen was central nervous system malformations (66.13%). Women with advancing age were more commonly associated with congenital malformations than younger women (highest risk in age group 25-29 years, 13.04%). Multigravida women had higher risk than primigravida. Women belonging to rural population were at higher risk than the women belonging to urban population (7.15% and 6.5% respectively). Women of lower middle class were found to have highest proportion of malformed babies (41.94%). 8.06% of women with congenital malformations had previous history of congenital malformations and 3.22% had history of previous 2 or more abortions. Mothers, who were unbooked cases, had higher incidence of congenital malformations than booked cases (7.66% and 5.94% respectively). Conclusions: Congenital malformations pose a threat for survival of a newborn in the early neonatal period. Various maternal risk factors are associated with its occurrence. A rational and multidisciplinary approach with good communication between various specialties (obstetrician, radiologist, Pediatrician, Genetic specialist and pathologist) and parents is essential. Regular screening for high risk mother’s subject should be done for early diagnosis and timely management of such cases.