Nuclei of the circadian visual system are extensively innervated by serotoninergic neurons and rhythmicity is modulated by the serotoninergic system. This study investigated the temporal relationships between prenatal origins of serotoninergic cell groups and perinatal innervation of structures in the hamster circadian visual system as well as in the remaining diencephalon. Serotonin-immunoreactive (5-HT-IR) neurons of the B4-B9 complex were first seen on embryonic day 8 (E8). The number of neurons increases sharply by E10 when the first 5-HT-IR cells are evident in the medulla (B1-B3 complex). The distribution of serotoninergic neurons in the hamster brainstem is generally adult-like by E14. Thick 5-HT-IR fibers arch around the mesencephalic flexure at E10 and reach more rostral mesencephalic areas at E11. A branch of the medial forebrain bundle (MFB) projects ventrally toward the retrochiasmatic area; a second branch ascends along the fasciculus retroflexus. Fibers cross the midline in the supraoptic commissure by E12, other arrive in the lateral geniculate region, and a branch of the MFB extends toward the mammillary area. At E13, a periventricular medial thalamic branch of the MFB is seen, axons appear in the supramammillary commissure, and a fine fasciculus between the medial thalamus and intergeniculate leaflet is visible. Lateral, paraventricular, and retrochiasmatic hypothalamic areas and centro- and dorsomedial thalamus are densely innervated at E14. The mammillary area and lateral geniculate body are moderately innervated, and the first fibers appear in the deep laminae of the superior colliculus. The innervation of the suprachiasmatic nuclei, periventricular hypothalamus, and superficial layers of the superior colliculus occurs postnatally. The results are consistent with serotoninergic system development in other species.