Habituation is a form of non-associative learning that is characterized by a decrease in responsiveness to a repeatedly presented stimulus. A useful model of mammalian habituation is the head-shake response (HSR), a rapid twisting of the head about the anterior-to-posterior axis elicited by a stream of air to the ear. The behavioral properties of HSR habituation include sensitivity to rate of stimulus presentation and a very predictable pattern of spontaneous recovery, suggesting that a neural timing mechanism is involved. One possible candidate is the suprachiasmatic nucleus (SCN) of the hypothalamus which utilizes "clock genes" to generate daily rhythms in behavior. To test this hypothesis, the effects of SCN lesions on habituation and recovery of the HSR were assessed across four inter-session intervals (ISI: 5 min, 2, 24, and 48 h) in rats. SCN-lesioned animals showed a significant decrease in responsiveness within sessions and impaired spontaneous recovery with the 24h ISI condition. The present findings suggest that the SCN may mediate temporal patterning of spontaneous recovery from habituation and is necessary in order to appropriately reset the animal to its pre-habituation level of responsiveness.