Technical Abstract: Scrapie is a naturally occurring fatal neurodegenerative disease of adult sheep and goats, one of a group of mammalian diseases known as transmissible spongiform encephalopathies or prion diseases. Immunoassays that identify disease-associated prion protein (PrP**Sc) are integral to the diagnosis of scrapie and other prion diseases. Results obtained by either immunohistochemistry or Western blot assay are generally adequate for the definitive diagnosis. Approved or accepted methods for Western blot diagnosis of transmissible spongiform encephalopathies requires the use of fresh or frozen non-fixed tissue samples, whereas formalin-fixed, paraffin-embedded tissue is required for the localization of PrP**Sc by immunohistochemistry. Since disparate processing methods are used for these accepted diagnostic techniques, separate tissue samples are collected from the same animal. Occasions arise in which there is either insufficient quantity of tissue available to complete analysis by both techniques or initial tissue processing is incompatible with one of the assays. Also, results between the assays may differ due to the vagaries of sampling, especially in case material containing moderate to low levels of PrP**Sc. This communication describes a method to conduct a Western blot assay from the same paraffin-embedded brainstem sample used for the immunohistochemical diagnosis of experimentally-induced sheep scrapie.