Johne's disease is recognised as an emerging problem in red and fallow deer in many countries. Prior to 1999 Johne's disease had not been identified in deer in Australia. Recently, however, five red deer herds in Victoria have been confirmed to be infected with the bovine strain of Mycobacterium paratuberculosis. These included two herds with high prevalence of infection and significant clinical disease in yearling animals. In particular mobs, more than 60% of animals were infected with M. paratuberculosis when tested by faecal culture and/or culture of tissues at slaughter. To minimise the risk of spread of Johne's disease between farms several Australian livestock industries have implemented Market Assurance Programs (MAP) which involve testing statistically significant samples of animals and adopting appropriate management practices to avoid introduction of infected animals into the herd. For the purpose of implementing a MAP for the deer industry, an ELISA and faecal culture have been evaluated. Three different conjugates were optimised for use in absorbed ELISA using plates and diluents from a commercial Johne's disease kit (Parachek). Pooling of faeces has also been examined to determine the sensitivity and feasibility of detecting infected animals from pools of various sizes. The receiver operating curves and performance of anti-deer, protein G and anti-bovine conjugates were similar although the protein G conjugate appeared to have a marginally higher relative sensitivity. Pooling of faeces for culture provides an opportunity to reduce the cost of herd testing.