-Colonic morphology and function change significantly during ontogenesis. In mammals, many colonic physiological functions are temporally controlled by the circadian clock in the colon, which is entrained by the central circadian clock in the suprachiasmatic nuclei (SCN). The aim of this present study was to ascertain when and how the circadian clock in the colon develops during the perinatal period and whether maternal cues and/or the developing pup SCN may influence the ontogenesis of the colonic clock. Daily profiles of clock genes Per1, Per2, Cry1, Cry2, Reverb␣, Bmal1, and Clock expression in the colon underwent significant modifications since embryonic day 20 (E20) through postnatal days (P) 2, 10, 20, and 30 via changes in the mutual phasing among the individual clock gene expression rhythms, their relative phasing to the light-dark regime, and their amplitudes. An adult-like state was achieved around P20. The foster study revealed that during the prenatal period, the maternal circadian phase may partially modulate development of the colonic clock. Postnatally, the absence and/or presence of rhythmic maternal care affected the phasing of the clock gene expression profiles in pups at P10 and P20. A reversal in the colonic clock phase between P10 and P20 occurred in the absence of rhythmic signals from the pup SCN. The data demonstrate ontogenetic maturation of the colonic clock and stress the importance of prenatal and postnatal maternal rhythmic signals for its development. These data may contribute to the understanding of colonic function-related diseases in newborn children. colon; circadian clock; clock gene; ontogenesis; circadian entrainment THE GASTROINTESTINAL TRACT begins functioning immediately after birth with demands to digest, absorb, and secrete water, electrolytes, and nutrients. Concurrently, the gastrointestinal tract also provides a selective barrier against the noxious environment of the gut lumen, which is continuously exposed to a variety of commensal and pathogenic microbes and antigens. During ontogenesis, the gut morphology and function undergo major modifications, which are already apparent during the prenatal period and continue during early postnatal development until weaning (for review, see Ref. 15). The primitive gut tube is established early prenatally, which coincides with the development of the enteric nervous system (3). After the gut tube is fully formed, the epithelium, mesenchyme, and lumen undergo expansion followed by epithelium reorganization. During that period, villi are formed in a rostrocaudal wave along the entire intestinal tract. Later, the spaces between the epithelial folds become populated by cells that represent proliferating compartments of the crypts (11). In rodents, colonic crypts are formed only after birth, and their morphological architecture further develops postnatally. Early postnatally, the immature colon is capable of transporting nutrients, such as carbohydrates and amino acids (1, 18), but this ability rapidly disappears with age. In rats, th...