ABSTRACT. An abnormal isoform of prion protein (PrP Sc ) was extracted from formalin-fixed paraffin-embedded (FFPE) tissues from sheep and analyzed by western blotting. PrP Sc immunoreactivity against anti-PrP monoclonal antibody T2, which recognizes discontinuous PrP sequences, differed amongst individual scrapie sheep cases. This may reflect structural differences in PrP Sc that have been formalin-fixed prior to their extraction. This study indicates that western blotting by using FFPE tissues is useful for the retrospective analysis of transmissible spongiform encephalopathies in which only formalin-fixed samples are available and in conducting transmissible spongiform encephalopathies surveillance where freezing system is insufficient. Transmissible spongiform encephalopathies (TSEs) are neurodegenerative disorders that affect humans and animals. Bovine spongiform encephalopathy (BSE) in cattle, scrapie in sheep and goats, and Creutzfeldt-Jakob disease in humans are examples of disorders included in this category [15]. Abnormal isoforms of prion proteins (PrP Sc ) are major components of pathogenesis [15], and the detection of PrP Sc is the key for TSE diagnosis. Western blotting (WB) and immunohistochemistry (IHC) are routinely used as confirmatory tests. Although WB is a convenient biochemical technique for the detection of PrP Sc , it is not always used because it requires frozen or fresh tissue samples.Scrapie is caused by many different prion strains, which are characterized by their incubation periods and neuropathology in inbred mice [5]. Strain-specific properties are attributed to the different conformations of PrP Sc [1,2,13,18]. The molecular profiles of PrP Sc in WB, including the glycoprofiles and molecular weights of proteinase-K (PK)-digested PrP Sc (PrPcore), are used for the classification of prion strains [3]. As such, it is known that the PrP Sc of BSE and that of scrapie in sheep can be distinguished using WB [14].In Mongolia, sheep and goats are the major livestock, with hide, skin, cashmere, and meat exports increasing every year. Because there have been no outbreaks of scrapie in Mongolia to date, it is of crucial importance that Mongolian sheep and goats are confirmed negligible of scrapie infection through consistent surveillance. Unfortunately, it is often difficult to collect and transport frozen brain tissues to laboratories for surveillance, which is also an issue experienced by BSE-affected countries. This is primarily because of geography, with Mongolia being a vast extent of land that includes both deserts to mountainous regions that can be subject to harsh climatic conditions. Nonetheless, pathological examinations are routinely used for the diagnosis of contagious diseases, including rabies and listeriosis.It has been reported that PrP Sc extracted from formalinfixed paraffin-embedded (FFPE) tissues can be detected by WB [12]. Because this technique could enable better TSE surveillance, we tested its usefulness on tissues from sheep scrapie cases for which frozen tissues wer...