To explore developmental changes in circadian organization of central and peripheral oscillators, circadian rhythms in clock gene expression were examined in 12 organs in transgenic rats carrying a bioluminescence reporter for Per2. Organ slices were obtained from different developmental stages starting at postnatal day 5 and tissue was cultured for more than 6 days. In addition, four organs were examined from embryonic day 20. Robust circadian rhythms in bioluminescence were detected in all organs examined. The circadian period in vitro was specific to each organ and remained essentially the same during development. The circadian peak phase on the first day of culture was significantly different not only among organs but also in the same organ. Three patterns in circadian phase were detected during development. Thus, during development, circadian phase did not change in the suprachiasmatic nucleus, adrenal gland and liver, whereas delay-shifts were seen in the pineal, lung, heart, kidney, spleen, thymus and testis. Finally, circadian phase advanced at postnatal day 10-15, and subsequently phase-delayed in skeletal muscle and stomach. Circadian amplitude also showed developmental changes in several organs. These findings indicate that the temporal orders of physiological functions of various organs change in the course of development. Such age dependent and organ specific changes in the phase relationship among circadian clocks most likely reflect entrainment to organ specific time cues at different developmental stages.