In classical scrapie, detection of PrPsc on lymphoreticular system is used for the in vivo and post mortem diagnosis of the disease. However, the sensitivity of this methodology is not well characterised because the magnitude and duration of lymphoid tissue involvement can vary considerably. The aim of the present study was to evaluate the efficiency of detecting PrPsc in rectal mucosa and third-eyelid biopsies. A total of 474 genetically susceptible sheep and 24 goats from three scrapie infected flocks were included in this study. A sample from rectal mucosa and a sample from third-eyelid lymphoid tissue were collected from each animal. Biopsy samples were fixed in formaldehyde and processed for immunohistochemical examination. Animals with negative biopsy results were studied more closely through a post mortem examination of central nervous and lymphoreticular systems and if there was a positive result, additional biopsy sections were further tested. The sensitivity of rectal mucosa and third-eyelid assays were 36% and 40% respectively on initial examination but increased to 48% and 44% respectively after retesting. The results of this field study show a high percentage of infected animals that do not have detectable levels of PrPsc in the biopsied lymphoid tissue, duemainly to the relatively high number of animals with minimal or no involvement of lymphoid tissue in the pathogenesis of the disease.