Prenatal ultrasonography is commonly used to detect fetal structural abnormalities. The aim of this study was to evaluate the reliability of fetal sonography in the detection of congenital gastrointestinal malformations (GIM). From a prospective database of all major structural fetal anomalies detected by ultrasound over 3 years in a region with a population of 3.5 million and an annual birth rate of 52,000, 294 reports of GIM were identified and reviewed. There were 220 confirmed cases of GIM, of which only 35 (16%) had been correctly identified prenatally. Of 84 prenatal diagnoses of GIM, only 35 (42%) were confirmed postnatally. Prenatal ultrasound was most reliable in the detection of duodenal obstruction (55% confirmed cases identified prenatally) and least reliable in malformations of the hindgut. Of 44 cases of nonspecific sonographic bowel abnormality (eg, echogenic bowel) with adequate follow-up, only 12 (27%) had a confirmed GIM after delivery. This study demonstrates that the prenatal ultrasound scan is still unreliable in the detection or exclusion of fetal GIM, and consequently clinicians involved in prenatal sonography or counselling should exercise caution in making such diagnoses.