Extracellular collections of abnormal filaments composed of prion proteins have been identified in the brains of scrapie-infected hamsters using immunoelectron microscopy. Some of the filaments were 1500 nm in length; generally, they exhibited a uniform diameter of 16 nm. Rarely, the filaments had a twisted appearance, raising the possibility that they are flattened cylinders or are composed of helically wound protofilaments. The prion filaments possess the same diameter and limited twisting as the shorter rod-shaped particles observed in purified preparations of prions. Both the filaments and rods are composed of PrP 27-30 molecules, as determined by immunoelectron microscopy using affinity-purified antibodies. The ultrastructural features of the prion filaments are similar to those reported for amyloid in many tissues including brain. These results provide the first evidence that prion proteins assemble into filaments within the brain and that these filaments accumulate in extracellular spaces to form amyloid plaques.