The purpose of this study is to compare the accuracy of prenatal ultrasound (US) and prenatal magnetic resonance imaging (MRI) in the diagnosis and characterization of congenital abnormalities of the genito-urinary tract and to determine if the additional information obtained by MRI may influence the management of the fetus. We retrospectively evaluate 15 cases of congenital genito-urinary tract anomalies detected by prenatal US and with echographic inconclusive diagnosis. We compare the MRI findings with the US findings and the final diagnosis, obtained from neonatal outcomes, imaging studies and pathology records. Fetal US diagnosis was correct in 9 cases (60%) and MRI in 13 cases (86.7%). Prenatal MRI revealed additional information to US in 9 cases (60%), which modified the initial US diagnosis in 5 cases (33.3%) and changed the therapeutic approach in 5 fetuses (33.3%). Fetal MRI was better than US in cases of oligoamnios and in fetuses with genito-urinary pathology concerning the pelvic and perineum region. We believe that MRI should be considered as a complementary diagnostic method in cases of echographic suspicion of congenital pathology of the genito-urinary tract and inconclusive prenatal US.