Thermoregulatory responses of rat pups with or separated from the dam were examined in relation to clock-controlled genes in the suprachiasmatic nucleus (SCN). During the nursing period, the decreased incidence of maternal contact with the pups was correlated inversely with the rising body temperature of the dam under the dark period. We determined the levels of Per2, Bmal1 and AVP mRNAs using RT-PCR in the SCN of pups after separation from the dam, which induces hypothermia. The Per2 changes were coordinated with the body temperature decrease after separation from the dam. In adult rats, the body temperature drop induced by pentobarbital administration was larger during the light than in the darkness. The alpha-and g-enolase, LDHa and LDHb mRNA, which are coupled with the metabolic state, were measured simultaneously with the clock related gene mRNAs, following hypothermia in pups on postnatal day 6. After dam separation, the Per2 and Bmal1 levels in pups increased after 1 h during the dark period, while AVP decreased after 9 h during the light period. The results indicate that the nursing dam influences Per2, Bmal1 and AVP mRNA transcriptions in the pup SCN through hypothermia (non-photic stimulation) induced by separation from the dam.