A rare case of segmental hypoplasia of the basilar artery is described in a 49-year-old man with transient vertebrobasilar ischemia, explored by magnetic resonance imaging (MRI) and digital angiography (DA). The embryology, clinical relevance and magnetic resonance findings of this arterial anomaly are discussed, with a review of six previously reported cases. Segmental aplasia was suggested in our case by magnetic resonance, and subsequently confirmed not only by time-of-flight magnetic resonance, but also by DA. Only ultrathin-slice T2-weighted images revealed the real finding of basilar artery hypoplasia. This sequence, not employed in previously reported cases, is mandatory to allow a clear differential diagnosis between basilar artery aplasia and hypoplasia.