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Prion diseases such as bovine spongiform encephalopathy, chronic wasting disease, and scrapie pose serious risks to human and animal health due to a host of disease-specific factors, including the resistance of infectious prions (PrPSc) to natural degradation and to most commercial inactivation procedures. In an attempt to address this concern, a mouse model was used to compare the efficacy of an alkaline hydrolysis process with a simulated continuous-flow rendering treatment for disposal of PrPSc-infected biological material. Female C57/BL6 mice (N = 120) were randomly divided into 4 treatment groups (n = 30), and each mouse was injected intraperitoneally with their designated treatment inoculum. Treatment groups 1 and 2 served as the positive and negative controls, respectively. Group 3 was inoculated with rendered scrapie-positive mouse brain material to investigate the effectiveness of simulated continuous-flow rendering practices to reduce or eliminate PrPSc. Group 4 was inoculated with hydrolyzed scrapie-positive mouse brain material to determine the sterilizing effect of alkaline hydrolysis on PrPSc. Mice were monitored for overt signs of disease, and those showing clinical signs were killed to prevent undue suffering. Brains were obtained from all mice that died (or were killed) and analyzed with an ELISA for the presence of PrPSc. Results indicated that the simulated continuous-flow rendering treatment used for preparing the rendering treatment group inoculum failed to completely eliminate PrPSc. Rendering delayed, but did not stop, clinical mouse-adapted scrapie transmission. Compared with positive controls, the rendering treatment group experienced an approximate 45-d average delay in days to death (250 vs. 205 d for positive controls; P < 0.0001) and a death loss of 73.9% (P = 0.0094). Positive controls suffered 100% death loss. The results validated the efficacy of the alkaline hydrolysis treatment to inactivate all PrPSc because no alkaline hydrolysis treatment group mice succumbed to the disease (P < 0.0001). Based on our results, alkaline hydrolysis should be considered by the animal rendering and beef packing industries as an alternative to incineration, landfill burial, and rendering for disposing of biological material potentially infected or contaminated with prion disease.