Intraneuronal prion protein (PrP) immunoreactivity (INIR), which might represent the non-pathological, cellular form of PrP, needs to be distinguished from disease-associated deposits specific for prion disease (PrD). In adjacent sections of PrD and control brains we applied pretreatments, one of which enhances the immunoreactivity of disease-associated PrP, and another that enhances INIR. We observed an inverse correlation between the proportion of neurons with INIR and the intensity of disease-associated PrP immunoreactivity and severity of lesions. Additionally, we found large intracytoplasmic inclusion-like bodies in ballooned neurons in PrD cases. We noted that the 3F4 (epitope: amino acids 109-112) anti-PrP antibody labels more INIR than antibodies directed against amino acids 23-85 (BG4) or 140-180 (KG9) in PrD cases, in contrast to controls, but all antibodies immunolabel more INIR in PrD brains. The up-regulation of PrP might represent an early loss of function of the non-pathological form of PrP, in parallel with a neurotoxic effect of accumulating disease-associated isoform, as part of the pathogenesis of prion diseases.