Introduction: The pattern and prevalence of congenital GI anomalies may vary over time or with geographical location with proportions as low as 1% to as high as 45.2%.It usually manifest in the neonatal period, with symptoms and signs of gastrointestinal tract obstruction and can be life-threatening.Objective: The Objective of study was to know the incidence, prevalence and pattern of GI Malformation in neonates.Material and method: This retrospective study was conducted in the Department of Paediatrics’, Rajkiya Mahila Chikitsalaya Hospital, J. L. N. Medical College Ajmer, a tertiary care institute of Rajasthan, India from January 1991 to December 2020 over a period of 30 years.Results: A total of 2,65,596 live births , out of which 6725 were having congenital anomalies. The prevalence of congenital malformation was 253/10,000, Standard deviation(SD): 61.28, 95% confidence interval (CI):53.26-69.30.The prevalence of GIT anomalies was 28.50 /10,000 live births, SD: 6.43, 95% (CI): 25.98-31.02 and incidence of GI anomalies was 11.25%.. The most common GIT anomaly was Anorectal malformation including imperforated anus(20.60%) followed by Intestinal atresia (20.20%%),Oesophageal atresia with or without TEF (17.04%)..Conclusions:Imperforated anus was the most common GI anomaly. Early diagnosis and management can result in better outcome of newborns with congenital GI anomalies.