We conducted a long-term study of the circadian rhythms of temperature and sleep in the rat after lesions of the suprachiasmatic nuclei (SCN). Brain temperature was measured with thermistors and sleep-wake was scored on the basis of continuously recorded EEG using a computerized system. Rats with complete SCN lesions did not exhibit circadian rhythms in constant dim illumination. Rats with partial SCN lesions generated weak and variable free-running rhythms, and when exposed to a light-dark cycle, some showed a reduced amplitude and altered waveform relative to normal rats. A few rats with partial SCN lesions showed a recovery of function. There was little difference between the circadian rhythms in temperature and waking, and these measures responded similarly to all lesions. Thus, no support was found for the notions that anatomically distinct oscillators control the circadian rhythms of temperature and activity, or that an oscillator outside of the SCN controls the circadian rhythm of temperature.