The afferent connections of the hypothalamic suprachiasmatic nucleus (SCN) of the golden hamster were examined using horseradish peroxidase (HRP) as the retrograde tracer molecule. Unilateral iontophoretic deposition of HRP into the SCN labeled ganglion cells bilaterally in the retinae. The labeled ganglion cells all had large somata and were randomly distributed across the retina. A similar number were labeled in each retina, which contrasted with the findings from injections into the optic chiasm and lateral geniculate body. Chiasm and geniculate injections both labeled three classes of ganglion cell (small, large, and giant) predominantly in the contralateral retinae. Telencephalic afferent projections to the SCN included the ventral subicular cortex and the septum. Notable diencephalic afferents included the dorsal lamina of the internal division of the ventral lateral geniculate nucleus (vLGN); the ipsilateral input was twice that of the contralateral projection. The same region of the vLGN was also noted to be reciprocally connected to the contralateral vLGN. The thalamic paraventricular nucleus was also heavily labeled but only ipsilaterally. Of functional significance, the SCN was discovered to innervate its contralateral homologue. Other less numerous afferents in the midbrain included the dorsal and median raphe nuclei and the dorsal nucleus of the lateral lemniscus. The afferent projections to the SCN determined in this study are discussed in regard to the known physiological role of the SCN as part of the circadian clock system.