Morphometric studies of the brains of seven Holstein-Friesian cows affected with bovine spongiform encephalopathy (BSE) and five control cows are reported. The numbers of neurons were counted in five selected neuroanatomical nuclei, namely the vestibular complex and red nucleus, both of which consistently show a high degree of neuronal perikaryonal vacuolation, the dorsal vagal nucleus, which shows inconsistent perikaryonal vacuolation, and the caudate and hypoglossal nuclei, which do not usually show vacuolation. The vestibular complex of BSE-affected cattle contained about half the number of neurons present in the controls. No statistically significant neuronal loss was demonstrated at other sites. These results confirm previous findings, showing that neuronal loss is a significant feature of BSE and may therefore contribute to the development of the clinical disease. No association was found between the duration of clinical signs and the number of remaining neurons or the extent of the vacuolation. However, the absence of such association should be viewed cautiously as there was substantial variation in neuronal populations between individuals. © 1994, Academic Press Limited. All rights reserved.