Purpose: To assess the prenatal prevalence of congenital malformations and the different types and to determine rate of perinatal mortality. Design: Cross-sectional study. Setting: Tertiary care centre. Materials and Methods: During the reporting period from August 2013 to September 2015, 6,432 ultrasound examinations were conducted in 2,832 pregnant women, out of whom 2,689 deliveries occurred in the referral center. Results: The authors diagnosed 119 cases with 154 congenital malformations (isolated: 82.35% cases; complex: 17.65% cases). The prenatal prevalence of congenital malformations was 54.38 for each 1,000 pregnancies, whereas the birth prevalence was 51.15 for each 1,000 births. The perinatal death rate was 35.29% (complex 73.68% and isolated 26.51%). The average maternal age of pregnant women was 29.94 years. Overall, the most widely observed congenital malformations involved circulatory system (20.78%), followed by musculoskeletal system (16.23%), followed by nervous system (12.34%), eye, ear, face, and neck (11.04%), cleft lip and cleft palate (7.79%), digestive system (7.79%), genital organs (6.49%), chromosomal abnormalities (5.84%), urinary system (4.55%), others (3.89%), and respiratory system (3.25%). Conclusion: The present study demonstrated that majority of perinatal deaths were due to complex congenital malformations. In turn the most common malformations included congenital heart diseases, neural tube defects, cleft lip/cleft palate, and polydactyly.