Timing of the circadian clock of the suprachiasmatic nucleus (SCN) is regulated by photic and non-photic inputs. Of these, neuropeptide Y (NPY) signaling from the intergeniculate leaflet (IGL) to the SCN plays a prominent role. Although NPY is critical to clock regulation, neither the mechanisms modulating IGL NPY neuronal activity nor the nature of regulatory NPY signaling in the SCN clock are understood, as NPY release in the SCN has never been measured. Here, microdialysis procedures for in vivo measurement of NPY were used in complementary experiments to address these questions. First, neuronal release of NPY in the hamster SCN was rhythmic under a 14L : 10D photocycle, with the acrophase soon after lights-on and the nadir at midday. No rhythmic fluctuation in NPY occurred under constant darkness. Second, a behavioral phase-resetting stimulus (wheel-running at midday that induces IGL serotonin release) acutely stimulated SCN NPY release. Third, bilateral IGL microinjection of the serotonin agonist, (+/-)-2-dipropyl-amino-8-hydroxyl-1,2,3,4-tetrahydronapthalene (8-OH-DPAT) (another non-photic phase-resetting stimulant), at midday enhanced SCN NPY release. Conversely, similar application of the serotonin antagonist, metergoline, abolished wheel-running-induced SCN NPY release. IGL microinjection of the GABA agonist, muscimol, suppressed SCN NPY release. These results support an intra-IGL mechanism whereby behavior-induced serotonergic activity suppresses inhibitory GABAergic transmission, promoting NPY activity and subsequent phase resetting. Collectively, these results confirm IGL-mediated NPY release in the SCN and verify that its daily rhythm of release is dependent upon the 14L : 10D photocycle, and that it is modulated by appropriately-timed phase-resetting behavior, probably mediated by serotonergic activation of NPY units in the IGL.