In three New South Wales dairy cattle herds with endemic Johne's disease, prevalence rates by faecal culture were determined to be 11%, 18% and 19% respectively. Whole herd faecal culture was shown to detect markedly more infected cattle than whole herd testing by the EMAI absorbed ELISA, particularly in the two herds with greatest prevalence. In the three study herds, five methods for whole herd faecal culture were compared in each. These included two methods based on primary culture on Herrold's egg yolk medium with Mycobactin J (HEYM): (1) conventional decontamination with sedimentation and primary culture on HEYM; (2) Whitlock decontamination and culture on HEYM. The remaining three methods were based on radiometric (BACTEC) culture: (3) decontamination and filtration to BACTEC medium; (4) modified Whitlock decontamination to BACTEC medium and (5) Whitlock decontamination to BACTEC medium. For BACTEC cultures, two methods were compared as confirmatory tests for M. paratuberculosis: mycobactin dependence on conventional subculture to HEYM and IS900 PCR analysis of radiometric media. Among 179 cattle tested simultaneously by all 5 culture methods, 38 cattle were confirmed to be shedding M. paratuberculosis and a further 3 were suspected to be shedding M. paratuberculosis. In identifying shedder cattle, method 5 was the most sensitive, followed by methods 2, 4, 1 and 3 was the least sensitive. The number of BACTEC cultures confirmed to contain M. paratuberculosis was similar for the two methods used. Reliability of diagnostic methods (clinical examination, faecal culture, allergic and serological tests) in paratuberculosis of cattle and sheep during the eradication and control programme from 1988-1998.