CS mice exhibit a spontaneous splitting in the circadian rhythm of locomotor activity under constant darkness, suggesting that they contain two weakly coupled oscillators in the circadian clock system regulating locomotor activity rhythm. In order to clarify whether the two oscillators are located in the suprachiasmatic nucleus (SCN), a site of the master circadian pacemaker in mammals, circadian rhythms in mRNA of mouse Period genes (mPer1, mPer2 and mPer3) in the SCN and cerebral cortex were examined during rhythm splitting by in situ hybridization. In the SCN, mPer1 and mPer2 showed a circadian rhythm with a single peak in both split and unsplit mice. The rhythms of mPer1 and mPer2 were slightly phase delayed during rhythm splitting in reference to the activity onset, but the phase relationship between the two rhythms was not changed. In the cerebral cortex, the expression of mPer1 and mPer2 underwent the bimodal fluctuation with peaks temporally corresponding to split activity components. The unsplit mice showed the circadian rhythms with a single peak. There was no difference in the mPer3 rhythms in either the SCN or the cerebral cortex between the split and unsplit mice. These results indicate that the circadian oscillations of mPer1, mPer2 and mPer3 in the SCN are not related to the rhythm splitting of CS mice. The split rhythms of the CS mice are suggested to be caused by uncoupling of oscillators located outside the SCN from the SCN circadian pacemaker.