Fetal magnetic resonance imaging (MRI) is a well-established second line imaging modality in identifying complex pathologies of the central nervous system (CNS), especially when ultrasound (US) findings are equivocal. It may enable an early and precise diagnosis, which is essential in terms of management of pregnancy and pre-, peri- and postnatal care. We present three cases with rare complex midline malformations of the CNS, diagnosed prenatally by fetal MRI. Two cases revealed holoprosencephaly; one case demonstrated rhombencephalosynapsis. In addition, we reviewed the literature and provide a summary of recent findings regarding cerebral midline development and discuss the advantages of fetal MRI.