Ontogeny (morphogenesis) describes the origin and the developement of an organism from the fertilized egg to its mature (adult) form. There have been studies in human infants, and especially Drosophila melanogaster, to observe how their circadian rhythmicity develop ontogenetically. The circadian ontogeny in animals is still a growing subject

In one study, Drosophila melanogaster born and reared in constant darkness exhibited circadian locomotor activity rhythms as adults. However, the rhythms of the individual flies composing these populations were not synchronized with one another. This lack of synchrony is evident in populations of flies commencing development at the same time, indicating that a biological clock controlling circadian rhythmicity in Drosophila begins to function without a requirement for light (a primary zeitgeber) and without a developmentally imparted phase. It is possible to synchronize the phases of rhythms produced by dark-reared flies with light treatments ending as early as the developmental transition from embryo to first-instar larva: Light treatments occurring at developmental times preceding hatching of the first-instar larva fail to synchronize adult locomotor activity rhythms, while treatments ending at completion of larval hatching entrain these rhythms. The synchronized rhythmic behavior of adult flies receiving such light treatments suggests that a clock controlling circadian rhythms may function continuously from the time of larval hatching to adulthood.

    In mammals, the circadian system is established and functional early in fetal life. Although the devlopmental timing differs between species, components of the circadian system like the suprachiasmatic nucleus (SCN: refer to the Mechanism page for more information about SCN) are active in the fetus. In precocious species several fetal bodily functions show 24-hr rhythms. The fetus, cloistered in the uterus, is still exposed to signals from the outside world that could convey circadian information. Environmental cues like sound traverse the abdominal and uterine wall. In some precocious species the innervation from the retina to the SCN is completed during fetal life and these fetuses can respond to external light while in utero. In addition it is quite clear that fetuses receive signals from their mothers and that these signals entrain fetal circadian rhythms and possibly convey photoperiod information. As a result of the interplay of maternally mediated and direct external information, the fetus learns to tell the time in utero. The adaptive advantages of acquiring these circadian capabilities during gestation is currently unknown. In nature, circadian rhythms time orderly periods of activity and rest in many physiological variables; in addition, circadian rhythms determine internal order of physiological functions within an individual. It may be advantageous for the fetus to time its physiological functions to that of the mother. To tell the time of the day may be important after birth. The mother could entrain the fetus to her own 24-hr rhythms thereby allowing adaptiation to maternal patterns of feeding behavior, for instance. Moreover, circadian rhythms probably prepare the fetus for postnatal events like day and night changes in ambient temperature. If properly informed, fetuses could prepare ahead of time for the warm or cold season to be encountered after birth. It is clear that in seasonal animals like the sheep and hamster, photoperiod definition learned in utero time the rate of development in order to reach puberty at an optimal time of year.
    Evidence gathered over the past decade indicates that the circadian timing system develops prenatally, with the SCN in the anterior hypothalamus, the site of a circadian clock, present by mid-gestation in primates. Recent evidence also shows that the circadian system of primate infants is responsive to light at very early stages (as early as 25 to 28 weeks’ gestation in humans) and that low-intensity lighting can regulate the developing clock. After birth, circadian system outputs mature progressively, with rhythms in sleep-wake cycles, body temperature, and hormone production generally developing between 1 and 3 months of age. The importance of light in regulation of circadian rhythm in infants is highlighted by the early establishment of rest-activity patterns that are in phase with the 24-hour light-dark cycle in preterm infants exposed to low-intensity cycled lighting. With the continued elucidation of circadian system development and influences on human physiology and illness, it is anticipated that consideration of circadian biology will become an increasingly important component of neonatal care.