The brains of 26 Bavarian bovines clinically suspected of bovine spongiform encephalopathy (BSE) were the subject of a neuropathological evaluation containing histopathology and immunohistochemistry. Six animals tested positive for BSE. In these six brains severe histological lesions that correlated with previous reports from the United Kingdom were observed. Immunohistochemistry with prion protein (PrP(Sc)), glial fibrillary acidic protein (GFAP) and synaptophysin were conducted on the mid-brain containing the red nucleus. All BSE-positive brains stained positively for PrP(Sc), and no plaques were observed. The BSE-affected brains showed a substantially more intense staining pattern for GFAP in comparison with the control groups, some of which were diagnosed with severe neuropathological disorders. Synaptophysin staining on BSE-positive brains was substantially reduced in the neuropil of the mid-brain, especially in the red nucleus. Twenty animals tested negative for BSE. The most common diagnoses were listeriosis, viral infections of unknown aetiology, brain oedema and hypomagnesaemia. These disorders may represent the most important clinical differential diagnoses for BSE in Bavaria.