A concurrent effect of age and puberty has hampered assessment of the influence of melatonin on human puberty. This study examined the pineal-puberty interaction in 41 subjects (ages 5–17 years) whose puberty was asynchronous from age (constitutional delay, hypopituitarism and idiopathic precocious puberty). Melatonin nocturnal profile was determined using blood samples drawn hourly by constant withdrawal. There was no significant trend for melatonin peak or time peak in pubertal or age groups. The linear correlation between age and melatonin peak was not significant. Thus, neither age nor puberty alone can account for the decline in nocturnal melatonin concentration observed across human development.