We performed magnetic resonance imaging of the pituitary gland in 354 children who were under the care of our pediatric neurological outpatient department. Among them, an empty sella was recognized in 11 children, who all showed normal hormonal results. The frequency of an empty sella was significantly high in idiopathic intracranial hypertension (4/4; P<0.0001) and nevoid basal cell carcinoma syndrome (3/5; P<0.0001). The ratio of an empty sella in children, excluding patients with idiopathic intracranial hypertension and nevoid basal cell carcinoma syndrome, is estimated to be 4/345 (1.2%), which is markedly lower than that in adults. Magnetic resonance imaging of the pituitary gland in children could provide important clues for the diagnosis of idiopathic intracranial hypertension or nevoid basal cell carcinoma syndrome.