Immunohistochemical techniques were employed to examine the changes in free ubiquitin within the hippocampus 1, 3, 7, 14, and 30 days after a unilateral perforant pathway lesion occurred in the rat brain. Immunoreactivity for ubiquitin was remarkably decreased in the cell body and proximal dendrites of neurons throughout the hippocampus ipsilateral to the lesion at 1 day post-lesion. At 3 days post-lesion, ubiquitin immunoreactivity was recovered in interneurons in the whole hippocampus as well as in mossy cells in the hilar region, although granule cells in the dentate gyrus and pyramidal cells in the CA1 subfield remained unlabeled, and pyramidal cells in the CA3 subfield demonstrated only weak immunoreactivity. In addition, we observed an increase in ubiquitin immunolabeling of the hilar neuropil ipsilateral to the lesion at 1 and 3 days post-lesion, and a decrease in immunolabeling in the inner portion of the molecular layer at 3 days post-lesion. All these alterations were transient, and by 7 days post-lesion, ubiquitin immunoreactivity was indistinguishable in the hippocampus ipsilateral to the lesion, compared to the controls. Immunoblot analysis also revealed a decrease in the amount of ubiquitin in the hippocampus ipsilateral to the lesion 1 and 3 days post-lesion. These data suggest that deafferentation of the perforant pathway results in transient reduction in free ubiquitin of the hippocampus, and that the ubiquitin system is involved in hippocampal plasticity following perforant lesions.