Prion is a term for the novel infectious agents which cause scrapie and Creutzfeldt-Jakob disease; these infectious pathogens are composed largely, if not entirely, of prion protein (PrP) molecules. No prion-specific polynucleotide has been identified. Considerable evidence indicates that PrP 27-30 is required for and inseparable from scrapie infectivity. PrP 27-30 is derived from a larger protein, denoted PrPSc. A cellular isoform, designated PrPC, and PrPSc are both encoded by a single copy chromosomal gene and both proteins appear to be translated from the same 2.1 kb mRNA. Monoclonal antibodies to PrP 27-30 as well as antisera to PrP synthetic peptides, react with both PrPC and PrPSc, establishing the relatedness of these proteins. PrPC is completely digested by proteinase K; PrPSc is converted to PrP 27-30 under the same conditions. Detergent extraction of microsomal membranes isolated from scrapie-infected hamster brains solubilizes PrPC but induces PrPSc to polymerize into amyloid rods. This procedure allows separation of the two prion protein isoforms and the demonstration that PrPSc accumulates during scrapie infection while the level of PrPC does not change. The prion amyloid rods generated by detergent extraction are identical morphologically, except for length, to extracellular collections of prion amyloid filaments which form plaques in scrapie- and CJD-infected brains. The prion amyloid plaques stain with antibodies to PrP 27-30 and PrP peptides. Prion rods composed of PrP 27-30 dissociate into phospholipid vesicles with full retention of scrapie infectivity. The murine PrP gene (Prn-p) is linked to the Prn-i gene, which controls the length of the scrapie incubation period. Prolonged incubation times are a cardinal feature of scrapie and CJD. While the central role of PrPSc in scrapie pathogenesis is well established, the chemical and conformational differences between PrPC and PrPSc are unknown but presumably arise from post-translational events.