Morning glory disc anomaly (MGDA) is a rare congenital malformation of the optic disc, which can be associated with midline craniofacial abnormalities, such as basal encephalocele. A female neonate presented with MGDA in the right eye, pendular nystagmus, hypertelorism, a flattened nasal root and cleft lip and palate. MRI revealed a basal encephalocele, agenesis of the corpus callosum and ventricular enlargement. MGDA combined with midline facial clefting should always lead to the suspicion of a basal encephalocele.