If the prevalence of bovine spongiform encephalopathy (BSE) varies among cohorts within a population, stratified analysis of BSE surveillance data may allow identification of differences in BSE exposure that are important with respect to the design and evaluation of disease prevention and control measures. In low BSE prevalence populations, however, surveillance at levels that meet or exceed international guidelines may provide insufficient statistical power to distinguish prevalence levels among cohorts. Furthermore, overstratification to account for hypothetical variability in the population may inflate uncertainty in BSE risk estimates.