Nonphotic phase shifts of the circadian clock in mammals are mediated by the intergeniculate leaflet (IGL) of the thalamus via a geniculohypothalamic projection to the suprachiasmatic nucleus. These shifts can be induced by arousing stimuli, such as wheel running, brain stimulation reward and foot shock. Because mesopontine cholinergic neurons are also activated by arousing stimuli, we tested the hypothesis that cholinergic input to the IGL mediates nonphotic phase shifts. Carbachol injected into the IGL of hamsters in their subjective day (CT8) induced phase advances similar to shifts that are induced by arousal at the same circadian time. Control injections of saline at CT8 did not advance phase similarly. Carbachol injections outside the IGL produced smaller shifts. Pre-injections of the muscarinic antagonist, atropine, reduced carbachol-induced phase advances relative to saline pre-injections. The results indicate that muscarinic input to the IGL can induce nonphotic phase shifts.