Introduction -- The suprachiasmatic nucleus (SCN) -- The endogenous rhythm of the SCN -- The SCN molecular clock -- Photic regulation of the circadian rhythm -- Retinal input – Neuroanatomy -- Neurotransmitters in the RHT -- Glutamate and PACAP -- Other neurotransmitters of the RHT -- RHT neurotransmitter receptors in the SCN.-Melanopsin - an irradiance detecting photopigment of the RHT -- Retinal input - Physiology -- Non-photic regulation of the circadian rhythms -- Midbrain raphe input - Neuroanatomy -- 5-HT and regulation of the circadian system -- The intergeniculate leaflet and the geniculohypothalamic tract – neuroanatomy -- Effects of NPY on circadian rhythm during subjective day -- NPY modulates light-induced phase shift during subjective night -- Summary.

Circadian rhythms are entrained daily by environmental photic and non-photic cues. The present review describes the anatomy and functional characteristics of the three major input pathways to the circadian clock mediating entrainment, the retino-hypothalamic tract (RHT), the geniculo-hypothalamic tract (GHT) and the midbrain raphe projection.