Effects of absence of nursing mothers on the circadian pacemaker of their offspring were examined by measuring clock genes, the rat Per1 (rPer1) and rPer2 expression rhythms in the pup suprachiasmatic nuclei (SCN). Neonate rats born to mothers kept under a 12-h light : 12-h dark cycle (LD) were blinded immediately after birth and exposed to periodic maternal deprivation where pups were deprived of their mothers during the light phase of 12-h for the first week of life. At postnatal day 6, the periodic maternal deprivation completely phase-reversed the circadian rhythms in expression of the clock genes in the pup SCN and in spontaneous locomotor activity after the pups were weaned at postnatal day 21. The periodic maternal absence also altered the patterns of stress-related gene expressions such as corticotropine-releasing hormone, arginine vasopressin, and glucocorticoid receptor in particular brain areas of the mother-deprived pups at P6. These findings indicate that periodic absence of the nursing mother in the first week of life produces a resetting effect on the neonatal circadian clock and induces stress responses in the hypothalamus-pituitary-adrenal axis.