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Central nervous system (CNS) abnormalities cause about 40% of infant deaths in the first year of life. In case of the detection of abnormalities by ultrasound, a pregnant woman should be offered prenatal magnetic resonance imaging (pMRI). The aims of our study were: (1) to evaluate the effectiveness of pMRI in the diagnosis of selected fetal CNS defects; and (2) to assess the possibility of replacing postnatal tests with prenatal magnetic resonance. The prospective and observational study was conducted between 2014 and 2017 at the University Hospital in Krakow. Patients with suspected CNS defects of the fetus were qualified for pMRI in the third trimester of pregnancy. Sixty patients were included in the study group. Prenatal MRI was characterized by low accuracy in the diagnosis of complex brain defects. Cohen's kappa coefficient κ = 0.21 (95% CI 0.00–0.46). No evidence was found suggesting the replacement of postnatal tests with pMRI. MRI was characterized by low consistency of diagnoses in the case of complex brain defects. The possibility of replacing postnatal studies with pMRI was not supported. [ABSTRACT FROM AUTHOR]