The intergeniculate leaflet (IGL) is considered involved in nonphotic shifting of the circadian clock through a direct connection, the geniculo-hypothalamic tract. The brain areas mediating nonphotic arousal to the hamster IGL have not been thoroughly investigated by both retrograde and anterograde tracing. We, therefore, reinvestigated the IGL afferent connections with the retrograde tracer Cholera toxin B and subsequently verified the results with the anterograde tracer Phaseolus vulgaris-leucoagglutinin. We also defined a subset of neurons projecting to the IGL that were activated by arousal using c-Fos immunocytochemistry. Apart from a dense afferent projection from the retina- and the contralateral leaflet, there were ipsilateral projections from other structures: layer V and VI of the prefrontal cortex, the zona incerta, the magnocellular part of the subparafascicular nucleus, the dorsal raphe nucleus, the locus coeruleus, and the cuneiform nucleus. Dense bilateral projections to the leaflet from the pretectal nuclei were found. Hypothalamic afferents were observed dorsal to the suprachiasmatic nuclei, in the retrochiasmatic area (RCh) and in the ventromedial hypothalamic nuclei. All of these projections were confirmed by anterograde tracing. Furthermore, arousal (wheel-running) induced c-Fos in neurons projecting to the IGL (prefrontal cortex, RCh, pretectum). Taken together, the data strengthen the view that the IGL integrates photic and nonphotic information.