Background: Magnetic resonance imaging (MRI) is of paramount importance for evaluating the hypothalamo-pituitary axis in children. Methods: We summarize the main points of the MRI technique, and describe the normal appearance of the hypothalamo-pituitary axis as a function of age and pubertal status. The most frequent causes of non-tumoral hypopituitarism include anterior pituitary deficiency (growth hormone deficiency may be isolated or associated with other anterior pituitary hormone deficiencies, with or without other malformations, and related to a known genetic abnormality in some cases), isolated hypogonadotropic hypogonadism and posterior pituitary deficiency with or without anterior pituitary hormone deficiency (central diabetes insipidus may be observed without tumor development). Results: We describe in detail the appearance of the adenohypophysis, the pituitary stalk and the neurohypophysis, correlations with hormone deficiencies, the abnormalities that may be associated and progression over time for each condition. Conclusion: An accurate description of hypothalamo-pituitary axis abnormalities is necessary for accurate diagnosis and prognosis evaluation, with certain features suggestive of particular diseases and some prognostic data correlated with phenotype.