What the media has termed as Mad Cow disease is a form of Transmissible Spongiform Encephalopathy (TSE). It is also known as a prion disease and occurs when the normal prion protein in the brain misfolds. This is thought to induce other prion proteins around it to misfold, leading to brain degeneration. Scrapie is a form of TSE in sheep; primarily infecting the central nervous and lymphoreticular systems. There is currently little explanation for why the process occurs, although, studies show that cytokines may be involved. Scrapie will not readily cause disease in normal mice. However, transgenic mice can be infected. These transgenic mice have a prion gene knockout with an insertion of the sheep version of the prion gene, which makes them susceptible when directly infected with scrapie prions. To further our understanding of prion diseases, we aimed to learn more about its source material, transmission, host genetic markers, and immune response with the help of a transgenic mouse model. We challenged transgenic mice with scrapie via the intracerebral route and observed them for signs of disease. Certain tissues were collected and analyzed at multiple points of infection for infectivity, potential co-localized proteins, cytokine dynamics, and growth factors. Various cytokine levels could increase, decrease, or stay the same throughout the infection period. This will enable a better characterization of immune response to prion disease and potentially provide a measure of disease progression using blood cytokine levels.