Background: Perinatal outcome is one of the major indicators of evaluating health care system of a country. Congenital defects form important components of this parameter. The aim of the study was to determine the risk factors associated with congenital malformations in foetuses.Methods: All antenatal mothers whose foetuses were detected to have congenital defects on ultrasonography irrespective of period of gestation were enrolled for the study.Results: Eighty-six pregnant women with prenatally diagnosed fetal anomalies were enrolled for the study, out of which, 87.2% (N=75) belonged to 20-30 years age group. Majority of the subjects were educated till secondary school. Compared to primigravidae, the incidence of malformations was significantly higher in the multigravida group (69.8% vs 30.2% respectively). Thirty-eight (44.2%) mothers with malformed foetuses missed folic acid intake during early pregnancy. Only 40% mothers had prior history of abortions. Smoking was seen in 9% of subjects with malformations. Seven (8.3%) mothers had previous history of malformations and 5 (5.8%) reported a family history of malformations. Consanguineous marriage was observed in 4.7% of couples. Oligohydramnios or anhydramnios was associated with 11.6% foetuses, while polyhydramnios was seen in 53.5%. CNS malformations were seen in 57% of foetus, followed by genitourinary system malformations (9.2%).Conclusions: Tertiary level hospitals need to be upgraded with a dedicated multidisciplinary team of foetal medicine to cater to medical, clinical, surgical, preventive and therapeutic needs of malformed foetuses.