Background: Antenatal care in India is rising due to improvement in awareness; still few congenital malformations can be missed in routine check-ups. One lost baby due to birth defects raises questions like; did the malformation led to death, what was the exact nature of malformation, will it recur in next pregnancy and are there any preventive measures? Few congenital malformations can be diagnosed prenatally with ultrasonography techniques, various maternal serum assays, confirmation relies on actual examination of the fetus or neonate. These techniques cannot identify large proportion of congenital malformations for which perinatal autopsy remains the gold standard investigation. The result of a perinatal autopsy may have broad impact, in that obstetrical, fetal, maternal, paternal, and familial conditions may be uncovered. Methods:The descriptive analytical study was carried out in Department of Pathology of a tertiary care hospital from June 2014 to May 2016 for detection of congenital malformations in fetal and early neonatal autopsies in 5 years. Conclusion:Despite advances in imaging such as antenatal ultrasonography and serology, perinatal autopsy is superior and continues to play an important role in diagnosing congenital malformations. The findings of autopsy are not only of theoretical importance but also of practical significance to clinicians in the form of estimating the risk of recurrence and in genetic counseling.