Repetitive genomic nucleic acid sequences (RGNASs) have been detected in serum samples from both PrP(res) confirmed cows and cohorts and unexposed cattle. These RGNASs have polymorphisms that can be candidates for detecting subclinical disease processes. To confirm the presence of serum RGNAS polymorphisms in bovine spongiform encephalopathy (BSE), samples were obtained from an experimental study whereby cows were inoculated orally with BSE-infectious or control brain material. Fleckvieh/Brown Swiss cattle were fed 100 g of either PrP(res)-positive brain stem macerate or normal brain material (controls). Serum samples were taken 40 months post-inoculation (15 infected, 6 control non-infected and 5 randomly selected normal animals). Approximately, 6e5 sequences were analysed and the results showed that serum RGNAS polymorphisms could be detected in all of the infected animals but not in the control animals. In addition, polymorphisms in serum non-RGNASs were detected in BSE-infected animals that differed significantly from the controls (P < 0.01). These data reveal the complexity of serum nucleic acid sequences that can be detected in 200 μl of serum and further add to the guidelines for using serum nucleic acids in diagnostics. In conclusion, RGNAS polymorphism detection may have general applications for the study of other emerging zoonoses.