Scrapie and chronic wasting disease (CWD) are prion diseases of particular environmental concern as they are horizontally transmissible and can remain infectious after years in the environment. Recent evidence suggests that the N-terminus of PrPSc, the infectious conformation of the prion protein, plays an important role in the mechanism of sorption to soil particles. We hypothesize that, in a prion-infected animal carcass, a portion of the N-terminus of PrPSc could be cleaved by proteinases in the brain at ordinary temperatures. Hamster (HY transmissible mink encephalopathy-infected), transgenic mice (CWD-infected), and elk (CWD-infected) brain homogenates were incubated at 22 and 37 °C for up to 1 month and then analyzed by Western blot using N-terminal and middle region monoclonal anti-PrP antibodies. For all three systems, there was a very faint or undetectable N-terminal PrP signal after 35 days at both temperatures, which indicates that full-length PrPSc might be rare in the brain matter of animal carcasses. Future studies on prion−soil interactions should therefore consider N-terminal-degraded PrPSc in addition to the full-length form. Both mouse and elk CWD PrPSc demonstrated greater resistance to degradation than HY TME PrPSc. This indicates that the transgenic mouse-CWD model is a good surrogate for natural CWD prions, but that other rodent prion models might not accurately represent CWD prion fate in the environment.