Individuals who suffer from idiopathic environmental intolerance attributed to electromagnetic fields (IEI-EMF) complain of a variety of adverse health effects. Troubled sleep remains a recurrent and common symptom in IEI-EMF individuals. Melatonin, a circadian hormone, plays a major role in the sleep process. In this study, we compared levels of melatonin between a sensitive group (IEI-EMF, n = 30) and a non-sensitive control group (non IEI-EMF, n = 25) without exposure to electromagnetic sources. Three questionnaires were used to evaluate the subjective quality and sleep quantity: the Epworth Sleepiness Scale, the Pittsburgh Sleep Quality Index and the Spiegel Sleep Inventory. Melatonin was quantified in saliva and its major metabolite 6-sulfatoxymelatonin (aMT6s) in urine. Melatonin levels were compared by a two-way analysis of variance at various times between the control and IEI-EMF group. Despite significantly different sleep scores between the two groups, with a lower score in the IEI-EMF group (P < 0.001), no statistical difference was found between the two groups for saliva melatonin (P > 0.05) and urine aMT6s (P > 0.05). Bioelectromagnetics. 37:175-182, 2016. © 2016 Wiley Periodicals, Inc.