The preferred method to determine the prevalence of bovine spongiform encephalopathy (BSE) in a country is to use immunology-based rapid-tests. Though these tests are validated to detect C-type BSE disease–associated prion (PrPsc), test-specific properties may influence their ability to detect H- and/or L-type BSE PrPsc, where both are atypical from C-type PrPsc. Molecular characterization shows atypical BSE PrPsc to have a different sensitivity to proteinase activity and different affinities for certain prion-specific antibodies. It is important to understand how atypical BSE PrPsc may affect the performance of rapid-tests, which are typically dependant on the use of specific proteases and antibodies. The current study used experimentally generated C-, H-, and L-type BSE PrPsc to evaluate 3 tests used in various national BSE surveillance programs: an immunochromatographic assay, a standard sandwich enzyme-linked immunosorbent assay (stndELISA), and a PrPsc-conformation–specific ELISA (confELISA). Although BSE PrPsc type had some effects on rapid-test performance, analytical sensitivity for atypical BSE PrPsc on all 3 platforms was not significantly compromised. When testing for atypical BSE PrPsc, the 3 tests were able to meet the same requirements that the European Food Safety Authority set when evaluating the tests for C-type BSE PrPsc.