Idiopathic hypogonadotropic hypogonadism (IHH) is a well-known disorder apart from its pathogenesis, which is still mostly unclear, even though a diverse subgroup of patients with hypogonadotropic hypogonadism and hyposmia/anosmia--the Kallman syndrome--have been partly linked to a mutated gene, known as kal-1 gene. In this study, we aimed to evaluate the sellar region of patients with IHH on magnetic resonance (MR). Pituitary MR of 120 male patients with IHH, diagnosed by a thorough endocrinologic assessment, were compared with pituitary MR of 49 healthy cases selected randomly who underwent detailed endocrinologic and neurologic evaluation and were assessed as healthy. Patients with IHH were diagnosed with microadenomas and irregularly contrasting pituitary (ICP), 18.2 and 10.7%, respectively. Although some anatomic variations were seen in healthy controls, microadenomas and ICP had solely been observed in patients with IHH and none in controls. Intact appearence of hypophysis in patients with IHH was significantly lower than in randomly selected healthy male subjects (p = 0.021). Mean infundibulum width of hypophysis and transverse diameter of posterior hypophysis were significantly broader in patients with IHH than in controls (both having p < 0.001), while mean hypophysis height and volume did not differ between groups. Results showed unusual incidence of pituitary abnormalities on pituitary MR in male patients with IHH. In conclusion, MR imaging is particularly useful in defining the morphological aspects of the hypothalamo - pituitary region in some endocrine disorders and other researchers might want to bear our findings in mind when performing MR evaluation of similar patient subgroups.