Eight cycling female rats were implanted with push-pull cannulae over the region of the suprachiasmatic nuclei (SCN) and allowed 7–10 days for recovery. Perfusion of the SCN continued in these freely behaving rats for 5–6 h of the light period and the subjective scotophase. The release of 5-hydroxyindoleacetic acid (5-HIAA) ranged from 10 to 350 pg 5-HIAA/min. Significantly, the amplitude and characteristics of the output of 5-HIAA were highly location dependent in that rostral cannulae placements revealed high amplitude changes with initial mean values of 40 pg 5-HIAA/min, which increased toward the dark phase to mean peak values of 195 pg 5-HIAA/min. Caudal cannulae placements revealed a low amplitude, high frequency, basal type of 5-HIAA release which did not increase toward the dark period (approximately 5 pg/min). 5-Hydroxytryptophan infusion resulted in a significant marked increase in the basal release of 5-HIAA confirming the biochemical viability of the area undergoing perfusion. These results suggest that the in vivo measurement of 5-HIAA from 5-hydroxytryptamine (5-HT) terminals in the region of the SCN could reflect discrete functional activity of serotonergic terminals within specific regions of the SCN in a freely behaving rat. Furthermore, the biochemical viability of these 5-HT terminals and the ability of the rat’s SCN to exhibit marked differential changes in 5-HT activity emphasizes the physiological relevance of this model system to study neuroendocrine events in freely behaving animals.