Significance In mammals, the suprachiasmatic nucleus (SCN) synchronizes circadian rhythms in cells throughout the body to the environmental light/dark cycle. We have developed a fluorescence-based technology that enables long-term monitoring of clock gene expression in particular brain nuclei and specific types of neurons at high temporal resolution, in freely moving mice, in a light/dark cycle. Using this system, we demonstrate the dynamics of Per2 and Cry1 transcriptional rhythms in SCN vasoactive intestinal peptide (VIP) neurons following an 8-h phase advance in the light/dark cycle.