The typical cyclic occurrence of cluster headache suggests the involvement of hypothalamic rhythm regulating centers in the pathogenesis of this primary headache. In previous studies, reduced 24-h plasma melatonin levels during the cluster period, loss of circadian melatonin secretion in remission, as well as permanently reduced excretion of urinary melatonin in both illness phases have been reported, supporting the hypothesis of a hypothalamic derangement. In this study, the 24-h urinary excretion of the main melatonin metabolite, 6-sulphatoxymelatonin, was evaluated in 20 cluster period cluster headache patients. Thirteen were retested 12 months later, in the same period of the year, during remission. Fourteen age- and sex-matched healthy subjects were the controls. As expected, significantly higher levels of 6-sulphatoxymelatonin were present in nocturnal urine than in day-time urine in controls, while in both cluster headache groups urinary levels of this metabolite did not differ between day and night. Nocturnal levels of 6-sulphatoxymelatonin were significantly lower in both cluster headache groups than controls. Day-time levels did not differ significantly between the groups. Altered excretion of urinary 6-sulphatoxymelatonin even during remission indicates that at least some of these anomalies are independent of the pain, and provides further evidence of involvement of the hypothalamic rhythm regulating centers in cluster headache.