Abstract Purpose This study was done to evaluate the role of fetal magnetic resonance imaging (MRI) in the study of gastrointestinal malformations in comparison to prenatal ultrasound (US). Materials and methods A prospective (2010–2012) study of 38 fetal MRI scans was performed on 38 fetuses between 24 and 38 weeks of gestation. All the fetuses had a US diagnosis of gastrointestinal anomalies. T2-weighted HASTE, T1-weighted fast gradient echo, TrueFISP and diffusion-weighted images of the fetal abdomen were obtained on a 1.5-Tesla magnet. All fetal MRI diagnoses were compared with postnatal US findings, autopsy or surgical reports. Results Fetal MRI was able to confirm the sonographic findings in nine of 38 fetuses (23.7 %), to provide additional information in 23 of 38 fetuses (60.6 %), to exclude the US diagnosis in five cases (5.2 %) and to change it in two cases (5.2 %). It was not able to characterize a case of gastric duplication and a case of abdominal cystic lymphangioma (5.2 %). Conclusions Fetal MRI can be used as a complementary imaging modality to US in prenatal evaluation of gastrointestinal anomalies and can be considered a valuable tool not only for confirming or excluding but also for providing additional information to fetal ultrasonographic findings.