In about 5% of the cows showing clinical signs of bovine spongiform encephalopathy (BSE) the histopathological examination is not conclusive. In order to rule out BSE in these cases, additional methods are necessary. For that reason, non-radioactive in situ hybridization (ISH) was performed using a riboprobe against the messenger RNA coding for the prion protein (PrP). In addition, a polyclonal antibody for immunohistochemistry (IHC) was generated against a synthetic peptide derived from bovine PrP. ISH and IHC were used to analyse brain sections of cattle suffering from BSE and various neurological diseases including four cows with clinically suspect but histologically unconfirmed BSE. ISH revealed no differences in localization, distribution and neuronal levels of PrP mRNA between BSE positive and negative cattle. However, there was a BSE-specific staining pattern in IHC allowing to exclude BSE the four suspected cases. Additionally, IHC for PrP is an elegant alternative to search for scrapie associated fibrils by electron microscopy.