We conducted a retrospective analysis on the clinical backgrounds and patient outcomes of 52 cases of congenital gastrointestinal atresia encountered in our institution in the past 28 years. These cases were divided into three groups: esophageal, duodenal, and intestinal atresia. Our evaluation revealed that the rate of polyhydramnios was significantly lower in the intestinal atresia group, but there was no significant difference in the rate of threatened preterm labor or preterm birth among all groups. Esophageal atresia had the highest perinatal mortality rate and the poorest neonatal prognosis. Conversely, there were no reported cases of chromosomal abnormalities in the intestinal atresia group, which had a good prognosis. Collectively, the prenatal diagnosis rate was 77% for all cases. Polyhydramnios as observed on ultrasonography, along with the appearance of gastric bubbles and bowel dilatation, and the use of fetal MRI all contributed to the prenatal diagnosis. However, when compared among groups, prenatal diagnosis and the accuracy of diagnostic rates by fetal MRI were significantly lower for esophageal atresia. Our analysis showed that ultrasonography and fetal MRI are useful tools for prenatal diagnosis of congenital gastrointestinal atresia, even though diagnosis is challenging in some cases. Since prenatal or postnatal prognosis depends on the site of the gastrointestinal tract obstruction, prenatal diagnosis has the significance of providing appropriate information to expectant parents, managing pregnancy, and facilitating neonatal treatment.