Melatonin is the principle hormone of the pineal gland.
It is normally made at night, but as the rhythm is generated in the biological clock of the brain (the suprachiasmatic nuclei or SCN) it is produced with a rhythm that deviates slightly from 24 hours even in continuous darkness. Because it is generated in the SCN the rhythm of melatonin is a marker of the phase of the clock. It is probably the best marker that can be measured at present.
Sufficently bright light suppresses melatonin, light dark changes (but also perhaps to a small extent other factors) synchronise the rhythm to 24 hours.
Abnormal melatonin production is seen when rhythms are disordered, as for example in shift work, jet lag, blindness, sometimes in old age and some diseases. It is associated with poor sleep and other problems.
The timing of melatonin production indicates the appropriate time for melatonin treatment or light treatment to adapt to phase shift or to treat circadian rhythm disorders.
6-sulphatoxymelatonin (aMT6s) is the major metabolite of melatonin i.e. the body converts melatonin mostly to aMT6s and then excretes it in the urine. aMT6s: