Studies of prion biology and diseases have elucidated several new concepts, but none was more heretical than the proposal that the biological properties that distinguish different prion strains are enciphered in the disease‐causing prion protein (PrP^Sc). To explore this postulate, we examined the properties of PrP^Sc from eight prion isolates that propagate in Syrian hamster (SHa). Using resistance to protease digestion as a marker for the undenatured protein, we examined the conformational stabilities of these PrP^Sc molecules. All eight isolates showed sigmoidal patterns of transition from native to denatured PrP^Sc as a function of increasing guanidine hydrochloride (GdnHCl) concentration. Half‐maximal denaturation occurred at a mean value of 1.48 M GdnHCl for the Sc237, HY, SHa(Me7), and MT‐C5 isolates, all of which have ∼75‐d incubation periods; a concentration of 1.08 M was found for the DY strain with a ∼170‐d incubation period and ∼1.25 M for the SHa(RML) and 139H isolates with ∼180‐d incubation periods. A mean value of 1.39 M GdnHCl for the Me7‐H strain with a ∼320‐d incubation period was found. Based on these results, the eight prion strains segregated into four distinct groups. Our results support the unorthodox proposal that distinct PrP^Sc conformers encipher the biological properties of prion strains.