The vacuolation, neuronal loss and gliosis that characterize human prion disease pathology are accompanied by the accumulation of an aggregated, insoluble and protease-resistant form (termed PrPSc) of the host-encoded normal cellular prion protein (PrPC). In variant Creutzfeldt-Jakob disease the frontal cortex and cerebellum exhibit intense vacuolation and the accumulation of PrPSc in the form of amyloid plaques and plaque-like structures. In contrast the posterior thalamus is characterized by intense gliosis and neuronal loss, but PrPSc plaques are rare and vacuolation is patchy. We have used sucrose density gradient centrifugation coupled with conformation dependent immunoassay to examine the biochemical properties of the PrPSc that accumulates in these different brain regions. The results show a greater degree of PrPSc polydisperal in thalamus compared with frontal cortex or cerebellum, including a subpopulation PrPSc molecules in the thalamus that have sedimentation properties resembling those of PrPC. Much effort has focused on identifying aspects of PrPSc biochemistry that distinguish between different forms of human prion disease and contribute to differential diagnosis. Here we show that PrPSc sedimentation properties, which can depend on aggregation state, correlate with, and may underlie the distinct neurodegenerative processes occurring in different regions of the variant Creutzfeldt-Jakob disease brain.