A growing body of evidence indicates the role of melatonin (MT) in the pathogenesis of multiple sclerosis (MS): It modulates immune function, alleviates oxidative stress and it is linked to seasonality of MS relapse. This report addresses the potential clinical relevance of circadian MT rhythms in relapsing-remitting MS (RRMS) patients. The study sample comprised of fifty-five RRMS patients and fifty age- and sex-matched healthy control (HC) subjects. Circadian salivary MT was measured non-invasively at 12 time points over day in participants' home environment. 6-Hydroxy-melatoninsulfate (MT sulfate) concentration in night-time urine was assessed as an estimate for nocturnal MT. Ratings for neurological disability, health-related quality of life (HrQoL), fatigue, depressive symptoms and sleep patterns were additionally obtained. There was no evidence for an overall disturbed MT rhythm in RRMS patients. However, lower MT levels within the first hour after awakening were associated with longer disease duration. MT levels only correlated moderately with neurological disability. Sleep disruptions were more common in patients than in controls and were associated with lower nocturnal MT sulfate levels. MT also correlated moderately with fatigue and HrQoL. We did not find evidence for a generally disturbed circadian MT rhythm in RRMS patients but longer disease duration was associated with significantly lower MT levels. Moreover, MT correlated with a series of clinical features. The exact nature of this relationship remains unclear and future studies are needed in order to determine whether MT could serve as a potential therapeutic target in MS. KEY MESSAGES: Melatonin acts as a free radical scavenger and modulates immune function. In multiple sclerosis, low melatonin levels were associated with acute exacerbations. Melatonin levels are not generally disturbed in multiple sclerosis patients. But lower levels are associated with disease duration and clinical aspects. Salivary melatonin after awakening might serve as a good measure of melatonin.