Abstract Background Congenital digestive malformations are a leading cause of infant mortality and morbidity. There are currently no reliable estimates of the number of children born with these malformations and the diversity of the underlying causes requires a range of preventive approaches. Thus, to estimate the prevalence and mortality of these pathologies and to determine the interest of prenatal diagnosis in Casablanca, we initiated this study. Methods This was a cross-sectional study conducted at the Ibn Rochd University Hospital in Casablanca from January 1, 2016, to December 31, 2019, among newborns with congenital digestive malformations diagnosed by a specialist in visceral and digestive surgery. Data related to pregnancy, delivery, and time of diagnosis were collected through the medical record and complemented by clinical and surgical data from the hospitalization registry. In addition to the descriptive analysis of the results, the statistical analysis included Log Rank tests and the Cox method. Results Among 33853 live births 140 cases (56 Esophageal Atresia, 12 Diaphragmatic Hernia, 29 Laporoschisis, 20 Neonatal Occlusion, and 23 Omphalocele) of neonatal digestive malformation (4,13/1000 live births) had been diagnosed, 19.3% (27/140) of which were diagnosed during the antenatal period with an estimated mortality of 2.86/1000 (96/33853) live births and a mean survival time of 9.14±0.92 days. There was no statistically significant association between the time of diagnosis (prenatal vs postnatal) of the disease and the risk of mortality (Log Rank test p = 0.781), and the differences in the association between prenatal diagnosis and infant mortality in the five neonatal digestive malformations were not statistically significant. Conclusions These results imply that survival may no longer be the most relevant outcome, or the best criterion, for assessing the impact of prenatal diagnosis on the outcome of neonatal digestive malformations. Key messages The prevalence and mortality of children with neonatal GI defects is high. Survival may be the most relevant outcome to assess the impact of prenatal diagnosis on the outcome of neonatal GI defects.