Idiopathic growth hormone deficiency is a disorder that is not clearly understood. We therefore evaluated the MR scans of 35 patients with idiopathic growth hormone deficiency in an attempt to define more clearly the abnormalities of the hypothalamohypophyseal axis, determine the frequency of these abnormalities, and determine whether a relationship exists between the MR findings and the patient's clinical history and endocrine function. Patients with MR abnormalities fell into two groups; those with an ectopic neurohypophysis (15 patients, or 43%), which consisted of a neurohypophysis near the median eminence, absence of the infundibulum, and absence of the normal posterior pituitary bright spot; and those with a small anterior pituitary gland (15 patients, or 43%), which was an isolated finding in five patients and associated with an ectopic neurohypophysis in 10 patients. Examination of endocrine function identified two groups of patients: those with multiple hormone deficiencies and those with isolated growth hormone deficiency. An ectopic neurohypophysis was present in 87% of the first group and 10% of the second group. The anterior pituitary dysfunction in those with an ectopic neurohypophysis was thought to be related to the absent infundibulum, which normally houses the portal system. Our MR findings demonstrated that over 40% of patients with idiopathic growth hormone deficiency have an ectopic neurohypophysis and absence of the infundibulum. We believe that the growth hormone deficiency in these patients is related to the absent infundibulum.