Recent work in multiple sclerosis, focusing on neuropathological abnormalities, found a frequent and severe hypothalamic involvement. The possible clinical implications are disturbances in sleep and sexual activity, depression, memory impairment and fatigue. Despite this there are no magnetic resonance imaging studies focusing on in vivo hypothalamic pathology in multiple sclerosis. Our objective was to investigate magnetic resonance imaging-detectable abnormalities related to pathological changes in the hypothalamus of patients with multiple sclerosis, and to subsequently explore the relationship with fatigue. We used T1 relaxation time as a sensitive measure of pathology. Using region of interest analysis, median T1 values in the hypothalamus were measured in 44 relapsing-remitting multiple sclerosis patients and in 13 healthy controls. Fatigue was assessed using the Fatigue Severity Scale, and patients were divided in two subgroups, fatigued and non-fatigued, according to Fatigue Severity Scale scores. We found a significantly higher T1 relaxation time in the hypothalamus of multiple sclerosis patients compared with controls (p = 0.027). There was a significant correlation between T1 values and fatigue severity (rho 0.437, p = 0.008), and median T1 values were different among the study groups. Our results show that pathological involvement of the hypothalamus in relapsing-remitting multiple sclerosis is detectable using magnetic resonance imaging, and that the pathology measured by quantitative T1 might reflect fatigue.