In accordance with controls instituted to protect the consumer from meat potentially infected with bovine spongiform encephalopathy (BSE), brain tissue emboli caused by the use of captive bolt gun (CBG) stunning have been identified as a potential public health risk that requires further investigation. As the natural occurrence of BSE in sheep remains uncertain we have investigated the frequency of brain tissue embolism associated with stunning by two types of CBG that are in commercial use in the United Kingdom. Blood samples collected from sheep following stunning were analysed by ELISA as well as by a combination of microscopy and immunocytochemistry. The combined positive results from each method of sample analysis were used to determine the frequency of brain tissue embolism in the sample population. The frequency of brain tissue embolism was found to be 23% in sheep stunned with a cartridge-activated CBG (95% confidence interval of 15.8-32.2%) and 14% in those stunned with a pneumatically activated CBG (95% confidence interval of 8.5-22%). The frequency of brain tissue embolism associated with the use of CBG stunning may represent a significant source of carcass contamination with brain tissue.