Information on the pathogenesis and tissue distribution of Atypical Bovine Spongiform Encephalopathy (BSE) in cattle through the study of field cases and experimental transmission studies is lacking. The latter are limited to transmission of Atypical BSE through intracerebral (i.c.) inoculation of cattle. All data currently available relate to the presence or absence of PrPSc, but do not quantify relative amounts of PrPSc or levels of infectivity. A laboratory protocol for further studies is recommended, to allow the assessment of the relative infectious titre, PrPSc accumulation and prion seeding activity in the tissues of cattle that developed H-BSE or L-BSE (using posterior brainstem as a reference). Tissues to be covered by those studies are categorised in three priorities, based on their inclusion in the list of specific risk material in cattle, on the presence of infectivity, or PrPSc presence, demonstrated in Atypical BSEs or other Transmissible Spongiform Encephalopathies (TSEs) in ruminants, and on the importance in terms of input into the food chain in the EU. The protocol provides details in terms of the minimum number of animals to be tested, processing and preparation of tissues, and methods to be used to identify abnormal PrP and quantify infectivity, also depending on the expected level of infectivity and amount of tissue available for analysis. It is recommended that, through the implementation of the protocol, information should also be obtained on the performance of currently validated rapid tests for TSE active surveillance in cattle/bioassay for detecting H-BSE and L-BSE agents.