Immediate early genes have gained widespread use as neural activity markers in studies of brain function. The recent development of cellular compartment analysis of temporal activity, which combines sensitive fluorescence in situ hybridization and laser scanning confocal microscopy, overcomes the lack of temporal resolution of standard methodologies and allows the tracking of distinct steps in the synthesis and processing of immediate early gene RNAs. Thus, this technique provides information about when individual neurons are activated and allows the visualization, within a single brain, of different neuronal populations engaged by two distinct experiences.