The symptoms of prion infection can take years or decades to manifest following the initial exposure. Molecular markers of prion disease include accumulation of the misfolded prion protein (PrP Sc ), which is derived from its cellular precursor (PrP C ), as well as downregulation of the PrP-like Shadoo (Sho) glycoprotein. Given the overlapping cellular environments for PrP C and Sho, we inferred that PrP C levels might also be altered as part of a host response during prion infection. Using rodent models, we found that, in addition to changes in PrP C glycosylation and proteolytic processing, net reductions in PrP C occur in a wide range of prion diseases, including sheep scrapie, human Creutzfeldt-Jakob disease, and cervid chronic wasting disease. The reduction in PrP C results in decreased prion replication, as measured by the protein misfolding cyclic amplification technique for generating PrP Sc in vitro. While PrP C downregulation is not discernible in animals with unusually short incubation periods and high PrP C expression, slowly evolving prion infections exhibit downregulation of the PrP C substrate required for new PrP Sc synthesis and as a receptor for pathogenic signaling. Our data reveal PrP C downregulation as a previously unappreciated element of disease pathogenesis that defines the extensive, presymptomatic period for many prion strains.