Habituation is defined as a decrease in responsiveness to a repeatedly presented stimulus. The head-shake response (HSR) demonstrates several fundamental properties of habituation including sensitivity to the frequency and intensity of stimulation, and spontaneous recovery. This response shows behavioral plasticity; however the neural plasticity presumed to underlie this behavioral phenomenon has only recently been investigated. The present study initially compared male and female rats and noted equivalent habituation and spontaneous recovery. A second experiment utilized female rats to test the hypothesis that habituation induces changes in neural plasticity. At inter-session intervals (ISIs) of 5 min, 2, 6, and 24 h following HSR habituation independent groups of rats received a second habituation experience, then tissue samples were immediately collected from hippocampal, prefrontal and piriform cortices, and cerebellum. Western blots indicated significant elevations in the expression of matrix metalloproteinase-3 (MMP-3) in hippocampal, prefrontal and piriform cortices at a delay interval of 2 h, and in the prefrontal cortex at 24 h in habituated rats. Increases in active and pro MMP-9 activity were measured by zymography in the hippocampus of habituated rats over yoked controls. Decreases in active MMP-9 activity were seen in the prefrontal cortex, and in pro MMP-9 in the piriform cortex, of habituated as compared with yoked control rats. No changes in MMP-3 or MMP-9 were observed in the cerebellum, and no changes in MMP-2 were seen in any of the four structures examined. These results suggest that habituation of the HSR produced elevations in MMP-3 expression in three of the four structures presently examined, accompanied by increased MMP-9 activity in the hippocampus and decreases in the prefrontal cortex. However, cues present in the test environment appear to have provoked elevations in MMP-3 and -9 independent of those accompanying habituation.