We immunohistochemically examined tissue sections from patients with prion protein (PrP) polymorphism using hydrolytic autoclaving enhancement. Abnormal PrP accumulations could be classified into plaque formations (plaque-type) and the diffuse gray matter stainings including synaptic structures (synaptic-type). Insertional polymorphism, a point mutation in codon 102 or 117/129, and a polymorphism in codon 129 (Val129) result in plaque-type PrP accumulations. The patients with codon 102 mutation also have synaptic-type PrP accumulations. However, a point mutation in codon 200 did not show plaque-type accumulations, and only showed synaptic-type PrP accumulations. Likewise, sporadic Creutzfeldt-Jakob disease patients without any known mutations only have synaptic type accumulations. These results imply that the primary structures of PrP influence the phenotype of prion diseases, especially in abnormal PrP distributions of the central nervous system.