The flock-level sensitivity of pooled faecal culture and serological testing using AGID for the detection of ovine Johne's disease-infected flocks were estimated using non-gold-standard methods. The two tests were compared in an extensive field trial in 296 flocks in New South Wales during 1998. In each flock, a sample of sheep was selected and tested for ovine Johne's disease using both the AGID and pooled faecal culture. The flock-specificity of pooled faecal culture also was estimated from results of surveillance and market-assurance testing in New South Wales. The overall flock-sensitivity of pooled faecal culture was 92% (95% CI: 82.4 and 97.4%) compared to 61% (50.5 and 70.9%) for serology (assuming that both tests were 100% specific). In low-prevalence flocks (estimated prevalence <2%), the flock-sensitivities of pooled faecal culture and serology were 82% (57 and 96%) and 33% (19 and 49%), respectively, compared to 96% (85 and 99.5%) and 85% (72 and 93%), respectively, in higher-prevalence flocks (estimated prevalence > or =2%). A Bayesian approach incorporating prior knowledge on flock-specificity of pooled culture produced similar estimates and probability intervals. These estimates assume conditional independence of the two tests, and therefore might have over-estimated the true flock-sensitivities of the tests if the flock-sensitivities of pooled faecal culture and serology were correlated. The estimated minimum flock-specificity of pooled culture when used for surveillance and assurance testing was 99.1% (96.9 and 99.9%). Surveillance and assurance programs in Australia are designed to provide a flock-sensitivity of 95% for an assumed prevalence of 2%. Pooled faecal culture is performing at close to this level--whereas the flock-sensitivity of serology appears to be lower than expected, particularly in lower prevalence flocks.