Empty sella syndrome (ESS) is a multicausal entity. The incidence of primary empty sella syndrome (PESS) in children with neuroendocrine dysfunction is not known. In the pediatric age group, frequency seems to have been underestimated. A total of 117 cases of neuroendocrine disorders, including complete growth hormone deficiency, primary hypothyroidism with pituitary resistance to thyroid hormone, obesity, central precocious puberty, hypothalamic hypogonadism and central diabetes insipidus, have been studied with computed tomography and/or magnetic resonance imaging of sellar region for etiologic evaluation. Twenty-one patients were found to have PESS. We noted a high incidence of PESS in children with neuroendocrine dysfunction (17.9%). Children with neuroendocrine dysfunction should be investigated with respect to PESS, and children with PESS recognized coincidentally should be studied with the particular consideration of subclinical neuroendocrine dysfunction.