Background: The pathophysiology of idiopathic intracranial hypertension (IIH), a condition characterized by raised intracranial pressure, is not well understood. Objectives: We hypothesized that the hypothalamus might exhibit alterations in patients with IIH, based on its established association with obesity and the potential role of hormonal and metabolic factors in IIH. Design: Retrospective single-center cohort study. Methods: Thirty-three individuals with IIH and 40 matched healthy individuals were studied, including levels of the hormones and proteins leptin, adiponectin, ghrelin, insulin, growth/differentiation factor 15 (GDF15), somatostatin, and melatonin. In vivo high-resolution T1-weighted magnetic resonance imaging (MRI) data were analyzed by quantification of hypothalamic volumes using a well-established segmentation method, separate for the anterior and the posterior hypothalamic subvolumes. An additional analysis was performed using age, gender, and BMI-matched subgroups of 20 IIH patients and 20 controls. Results: The analysis of laboratory values showed significantly increased insulin, leptin, and melatonin levels for IIH patients in comparison to controls, while adiponectin levels were decreased in IIH; however, only melatonin level differences could be confirmed in the analysis with BMI matching. There was no statistical difference in total hypothalamus volumes between IIH and controls, but the hypothalamic morphology was altered in IIH patients with a lower volume of the anterior part of the hypothalamus and a higher volume of the posterior part; these results were identical in the analysis of the BMI-matched groups. The correlation analyses between hormonal changes and hypothalamic morphology did not achieve significant results. Conclusion: In this exploratory study, morphological abnormalities of the hypothalamus were observed to be associated with the IIH complex, although the mechanism remains to be unraveled. These findings expand the metabolic phenotype of IIH, but further functional studies are necessary to corroborate these data.