Exposing an animal to light during the normal dark period of its daily cycle induces shifts in the animal's circadian rhythm of activity. These shifts are preceded by an increase in the expression of an array of immediate early genes in the suprachiasmatic nucleus, the location of the primary circadian clock in the brain. For most of these genes, little is known about the physiological significance of their expression in the SCN. In order to characterize the expression of these genes, laser capture microscopy, and real-time PCR were used to measure the time course of expression of immediate-early genes in the SCN after a 30-min light pulse during the early portion of the night. Most of the measured genes show peak expression shortly after the end of the stimulus and then decline back to baseline after 2h. However, a few genes, including Rrad, Egr3, and Jun, show a more sustained elevation in expression. Analysis of the function of light-induced genes in other cellular systems suggests a possible role for these genes in reducing the SCN to subsequent photic stimuli and in protecting the SCN from excitotoxicity.