The effect of brain lesion or surgical isolation of the neural circuit on SWS and PS circadian rhythm have been studied in female rats under a 14/10 light-dark schedule. Cortical EEG'S AND DORSAL NECK EMG were used to monitor SWS, PS and alertness in female rats. Intact and operated controls showed regular 4-5-day vaginal cycles and nocturnal sleep rhythm, but the night PS value on proestrus was lower than in other cycles. Following septal lesion, MPO roof cut, vaginal cycles and SWS rhythm were regularly maintained; however, the PS appearance at night, except during proestrus, increased (night PS peak). These results were similar to those for pinealectomized or ovariectomized female rats. A frontal cut of the MBH produced persistent estrus and disturbed both SWS and PS circadian rhythm. The suprachiasmatic-lesioned rats showed persistent estrus and disrupted SWS rhythm, but regularly maintained the circadian PS rhythm. The vaginal cycles and SWS rhythm in the fornical-transected rats were regularly maintained, but the PS rhythm was disturbed during diestrus and showed ultradian rhythm. From these results, it is suggested that the pineal hormone and the gonadal feedback mechanisms may be involved in the night PS peak and this mechanism may involve the septal- and amygdaloid-hypothalamic systems. A different neural mechanism exist for SWS and PS circadian rhythm; SWS rhythm involves the suprachiasmatic-basal hypothalamic system and PS circadian rhythm is related, in part, to the hippocampal-hypothalamic system.