Prion diseases are chronic and fatal neurodegenerative diseases characterized by the accumula-tion of disease-specific prion protein (PrPSc), spongiform changes, neuronal loss, and gliosis. Growing evidence shows that the neuroinflammatory response is a key component of prion diseases and contributes to neurodegeneration. Toll-like receptors (TLRs) have been proposed as important mediators of innate immune responses triggered in the central nervous system in other human neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. However, little is known about the role of TLRs in prion dis-eases, and their involvement in the neuropathology of natural scrapie has not been studied. We assessed gene expression of ovine TLRs in four anatomically distinct brain regions in natural scrapie-infected sheep and evaluated possible correlations between gene expression and patho-logical hallmarks of prion disease. We observed significant changes in TLR expression in scra-pie-infected sheep that correlate with the degree of spongiosis, PrPSc deposition, and gliosis in each of the regions studied. Remarkably, TLR4 was the only gene upregulated in all regions, re-gardless of the severity of neuropathology. In the hippocampus, we observed milder neuropa-thology associated with a distinct TLR gene expression profile and the presence of a peculiar microglial morphology, called rod microglia, described here for the first time in the brain of scrapie-infected sheep. The concurrence of these features suggests partial neuroprotection of the hippocampus. Finally, comparison of findings in naturally-infected sheep versus an ovinized mouse model (tg338 mice) revealed distinct patterns of TLR gene expression.