Background: Congenital malformations remain a common cause of perinatal deaths accounting for 10-15% in developing countries like India. They are the most severe disorders of the central nervous system. Although antenatal screening for congenital anomalies has been improved over the years, fetal autopsy remains the gold standard for the identification and confirmation of congenital malformations. The present study emphasizes the importance of perinatal autopsy for understanding the cause of death and also conformation of the antenatal diagnosis of the spectrum of various congenital CNS malformations. Methods: We studied 644 perinatal autopsies conducted in our hospital. The duration of the study was 5 years, from 1^st August 2015 to 31^st July 2020 that included all perinatal autopsies with gestational age of 22 weeks to less than 7 days. Results: Out of 644 perinatal autopsies 125 cases (19.4%) had congenital anomalies, of which 62 cases (9.6%) showed CNS malformations. The most common CNS anomalies encountered were anencephaly 14 cases (22.6%) followed by 10 cases (16.1%) each of spina bifida and meningocele, and 8 cases (12.9%) of meningomyelocele. In the present study, 6 (9.7%) cases of CNS malformations were associated with known syndromes namely Edward syndrome, Potter’s syndrome, and KlippelFeil syndrome. Along with CNS in 21 (33.9%) cases we observed associated malformations of other systems with 7 cases involving the musculoskeletal system, 3 cases involving the genitourinary system, and 5 (8.1%) cases showing multisystem involvement. Conclusion: Antenatal screening for congenital anomalies has been improved over the years. Even then fetal autopsy remains the gold standard for the identification and confirmation of congenital malformations. Understanding this gives valuable information that can be further helpful in the genetic counseling of the parents.