The cofactor preferences for in vitro propagation of the protease-resistant isoforms of the prion protein (PrPSc) from various rodent species were investigated using the serial protein misfolding cyclic amplification (sPMCA) technique. Whereas RNA molecules facilitate hamster PrPSc propagation, RNA and several other polyanions do not promote the propagation of mouse and vole PrPSc molecules. Pretreatment of crude Prnp(0/0) (PrP knockout) brain homogenate with RNase A or micrococcal nuclease inhibited hamster but not mouse PrPSc propagation in a reconstituted system. Mouse PrPSc propagation could be reconstituted by mixing PrPC substrate with homogenates prepared from either brain or liver, but not from several other tissues that were tested. These results reveal species-specific differences in cofactor utilization for PrPSc propagation in vitro and also demonstrate the existence of an endogenous cofactor present in brain tissue not composed of nucleic acids.