Cells infected with prions contain both prion protein isoforms cellular prion protein (PrPC) and scrapie prion protein (PrPSc). PrPSc is formed posttranslationally through the pathological refolding of PrPC. In scrapie-infected ScN2a cells, the metabolism of both PrP isoforms involves cholesterol-dependent pathways. We show here that both PrPC and PrPSc are attached to Triton X-100-insoluble, low density complexes or ''rafts.'' These complexes are sensitive to saponin and thus probably contain cholesterol. This finding suggests that the transformation PrPC --> PrPSc occurs within rafts. It also reveals the existence of rafts in late compartments of the endocytic pathway, where most PrPSc resides. When Triton X-100 lysates of cells were incubated at 37 degrees C prior to density analysis, PrPC was still found in buoyant complexes, although it now failed to sediment at high speed. This property was shared by another glycophosphatidyl inositol protein, Thy-1, and also by the raft resident GM1. In one ScN2a clone and in the brain of a Syrian hamster with scrapie, Triton X-100 extraction at 37 degrees C permitted resolution of PrPC and PrPSc into two distinct peaks of different densities. This suggests that there are two populations of PrP-containing rafts and may permit isolation of PrPC-specific rafts from those containing PrPSc. Our findings reinforce the contention that rafts are involved in various aspects of PrP metabolism and in the ''life cycle'' of prions.