Aims: To determine the risk associated with the use of carcase storage vessels on a scrapie infected farm. Methods and Results: A stochastic quantitative risk assessment was developed to determine the rate of accumulation and fate of scrapie in a novel low-input storage system. For an example farm infected with classical scrapie, a mean of 10(3.6) Ovine Oral ID(50)s was estimated to accumulate annually. Research indicates that the degradation of any prions present may range from insignificant to a magnitude of one or two logs over several months of storage. Conclusions: For infected farms, the likely partitioning of remaining prion into the sludge phase would necessitate the safe operation and removal of resulting materials from these systems. If complete mixing could be assumed, on average, the concentrations of infectivity are estimated to be slightly lower than that measured in placenta from infected sheep at lambing. Significance and Impact of the Study: This is the first quantitative assessment of the scrapie risk associated with fallen stock on farm and provides guidance to policy makers on the safety of one type of storage system and the relative risk when compared to other materials present on an infected farm.