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Background: COVID-19 was an infection that was capable of bringing the entire world to a standstill position within a period of days to months. Despite the advancements in the medical sector, the contagion was difficult to control and costed the lives of millions of people worldwide. Many short- and long-term effects are witnessed even to date in people that contracted the disease. Pregnant females had to suffer not only the devastating effects of the virus, but also the psycho-social impact of the lockdown. The impact of COVID-19 infection during pregnancy causing decreased antenatal care or hypoxemic episodes due to severe respiratory distress and whether it could lead to the appearance of congenital gastrointestinal malformation in neonates is still unclear. The aim of our study was to analyze if COVID-19 infection during pregnancy could increase the incidence of gastric malformations in neonates born from these women. Materials and Methods: We sifted the files of all neonates admitted into our hospital between January 2022 and December 2022, and based on inclusion and exclusion criteria, we included the cases having gastrointestinal congenital malformations during the COVID-19 pandemic. We performed a single-center, retrospective, observational descriptive study. We further divided the patients based on the anatomical location of the malformation. We also took down details of the evolution of pregnancy and whether the mother had contracted a SARS-CoV-2 infection during the pregnancy. Details regarding the Apgar score, days of intensive care admission, sex, and nutrition were the key findings studied. Results: A total of 47 neonates were found to have digestive anomalies, among which, based on the anatomical locations, the number of malformation cases found at the level of the esophagus were 15, while 16 occurred at the level of the pylorus; we found 12 cases of malformation of the duodenum, and four cases had malformation of the rectum. Out of these 47 neonates, 38.3% were females and 61.7% were males. A total of 58% were preemies, among which 9% had intra-uterine growth retardation (IUGR), and 42% were full-term newborns, among which 4% had intra-uterine growth retardation (IUGR). A total of 45% of the births were primiparous pregnancies and 55% were from multiparous females. A total of 14 mothers were found to have tested positive for COVID-19 during the course of pregnancy (p-value = 0.23); many had mild symptoms but were not tested. Conclusions: COVID-19 can affect the wellbeing of the pregnant female and their fetus. Larger studies can help gain extensive knowledge as to whether COVID-19 also has the potential to result in congenital gastrointestinal anomalies in children born from COVID-19 positive mothers. In our study, only a few infants born with this pathology were found to be born from COVID-19 positive mothers. Hence, it is difficult to conclude or exclude a direct correlation between the infection and the congenital malformations.