OBJECTIVE To evaluate the additional information of second trimester magnetic resonance imaging (MRI) compared with ultrasound in fetuses with identified or suspected non-CNS anomalies and to study the clinical impact of the MRI information on pregnancy management. METHODS Prospective study during 2003-2007. The fetal MRI examination was planned to be performed within 3 days after the ultrasound. METHODS Uppsala University hospital. METHODS Sixty-three women in whom the second trimester ultrasound identified or raised suspicion of fetal anomalies were included. METHODS Ultrasound was compared to MRI in relation to the final diagnosis, which was based on the assessment of all available data, including postpartum clinical follow-up and autopsy results. METHODS Evaluation of the additional information gained from MRI and the consequences it had on pregnancy management. RESULTS The mean interval between ultrasound and MRI was 2.6 days (range 0-15 days). In 42 (67%) women MRI was performed within 3 days. All MRI examinations were assessable. In 43 (68%) fetuses MRI provided no additional information, in 17 (27%) MRI added information without changing the management and in three (5%) MRI provided additional information which changed the management. All these three cases had oligohydramnios. In all six cases of diaphragmatic hernia MRI provided additional information. CONCLUSIONS Fetal MRI of non-CNS anomalies in the second trimester seems to be a valuable adjunct to ultrasound diagnosis of non-CNS anomalies, especially in cases of oligohydramnios and diaphragmatic hernia.