Introduction After a modification in its three-dimensional structure, a normal host-encoded prion protein is converted into an abnormal isoform that is termed a prion. Prions cause transmissible spongiform encephalopathies (TSEs), which are fatal neurodegenerative disorders such as Gerstmann-Straussler-Scheinker (GSS) syndrome and Creutzfeldt-Jakob disease (CJD) in humans, bovine spongiform encephalopathy (BSE) in cattle, and scrapie in small ruminants (1). Scrapie is the oldest prion disease of sheep, known about for 250 years, and therefore regarded as the prototype of other TSEs (2). The disease is characterized by long incubation periods from months to years, progressive vacuolization, and amyloid plaque formation in the central nervous system (3). It is thought that the cattle prion disease BSE, which can be transmitted to humans and causes a new variant of CJD (4), originated from the use of the scrapie-contaminated products in cattle nutrition (5). It is well described that the prion protein gene (PrP) modulates susceptibility to classical scrapie. Polymorphisms at codons 136, 154, and 171 of the PrP have strong influence on the development of the disease in sheep (6). According to the PrP genotype, classical scrapie risk groups from R1 (at lowest risk) to R5 (at highest risk) were designated in the UK in 2001 (7), and several EU member states and the USA have adopted selective breeding programs aiming to increase genetic resistance to scrapie (8). In 1998, an atypical type of scrapie was diagnosed in Norway. Its histopathological features were different from those of classical scrapie and it was termed Nor98 (9). In the following years, many atypical cases were reported, especially in European states (10,11). Further studies have shown that some PrP variants are also related to atypical scrapie susceptibility (12,13). The Karacabey merino, one of the major breeds of the sheep industry in Turkey, was developed by crossbreeding German mutton-wool merino rams with native Kivircik ewes in the 1930s (14). The breed has adapted well, especially to the South and North Marmara as well as the West Anatolia regions of Turkey. Purebred Karacabey Abstract: Scrapie, the oldest prion disease of sheep, has two types: classical and atypical scrapie. It was determined that some nucleotide polymorphisms in the PrP coding gene have affected classical and atypical scrapie susceptibility. Consequently, EU member states have established breeding programs aiming to increase genetic resistance of their flocks to classical scrapie. These breeding programs have primarily been implemented in economically important breeds. Thus, we investigated classical and atypical scrapie related PrP genotypes of the Karacabey merino breed, which is of great economic importance in western regions of Turkey. In relation to classical scrapie, three alleles