Pathologies of hypothalamus–hypophysis axis in children express different clinical presentations, regarding endocrine secretions of numerous hormones. Knowledge of embryology, anatomy, and physiology is mandatory to understand the main features of these diseases. MRI is the best tool to assess the anatomical characteristics of the malformative and acquired pathologies. The main clinical expressions are in relation with isolated GH or combined antehypophysis hormones deficiencies, troubles in relation with puberty development, diabetes insipidus; cranial hypertension and visual disturbances may also reveal the disease. Pathologies include developmental disorders, in relation, in most cases with trouble of embryological brain diverticulation, aplasia or hypoplasia of pituitary gland, pituitary stalk interruption. Intra- and suprasellar masses can be a craniopharyngioma, a germinoma, and, mainly after 10 years of life, a pituitary adenoma. Systemic and inflammatory diseases include Langerhans cell histiocytosis, and, rarely in children, lymphocytic hypophysitis, sarcoidosis, and tuberculosis.