Prion-infected cells accumulate a heterogeneous population of aberrantly folded PrP conformers, including the disease-causing isoform (PrPSc). We found that specific chemicals can modulate the levels of various PrP conformers in cultured cells. Positively charged polyamidoamines (dendrimers) eliminated protease-resistant (r) PrPSc from prion-infected cells and induced the formation of insoluble, protease-sensitive PrP aggregates (designated PrPA). Larger, positively charged polyamidoamines more efficaciously induced the formation of PrPA and cleared rPrPSc, whereas negatively charged polyamidoamines neither induced PrPA nor cleared rPrPSc. Although the biochemical properties of PrPA were shown to be similar to protease-sensitive (s) PrPSc, bioassays of PrPA indicated that it is not infectious. Our studies argue that PrPA represents an aggregated PrP species that is off-pathway relative to the formation of rPrPSc. It remains to be established whether the formation of PrPA inhibits the formation of rPrPSc by sequestering PrPC in the form of benign, insoluble aggregates.