Prion diseases are neurodegenerative disorders characterized by accumulation of an aberrantly folded isoform (PrP(Sc)) of the normal prion protein (PrP(C)). Using in situ hybridization and immunohistochemistry, we have studied changes in the expression of neuropeptides, acetylcholinesterase and tyrosine hydroxylase in CD1 and FVB wild-type mouse strains, as well as in PrP(C) null mice and in mice overexpressing PrP(C) following intracerebral inoculation with RML or Me7 prions. In the immunohistochemical analysis, neuropeptide Y (NPY), enkephalin and dynorphin-like immunoreactivities increased in mossy fibers of CD1 and FVB mice inoculated with either RML- or Me7 prions, whereas cholecystokinin-like immunoreactivity was decreased. These changes in peptide levels were paralleled by an increase in the transcripts in granule cells for neuropeptide Y, enkephalin, and cholecystokinin. However, the dynorphin transcript was decreased in the granule cells. The changes occurred more rapidly in PrP(C)-overexpressing compared to wild-type mice, and could not be found at all in PrP(C)-knockout mice. These changes in peptide expression, which mostly occur before appearance of symptoms of disease, may reflect attempts to initiate protective and/or regenerative processes.