Johne's disease, caused by infection with Mycobacterium paratuberculosis (Map), is an important bacterial disease affecting productivity in New Zealand farmed deer herds. In addition to clinical losses, subclinical infection results in reduced growth and reproduction. Deer differ from other species of farmed ruminants in that can present with clinical disease at a young age (8-12 months). Microbial culture of gut tissue obtained at necropsy has been the 'gold standard' for diagnosing Map infection. Diagnosis of infection in live animals continues to be a challenge. The Disease Research Laboratory's recently developed Paralisa™ test has good sensitivity (> 90%) and specificity (> 98%) for the detection of animals with Johne's disease. It has a lower sensitivity (75%) in diagnosing Map infected deer without lesions. The use of this test in severely infected deer herds can reduce the prevalence of reactors from high (>40%) to low levels (<5%) within 2-3 years and results in the elimination of clinical disease. As clinically detectable Johne's disease represents a minor proportion of the total number of Map infected deer within a herd, it is also important to have diagnostic tests that detect subclinically infected animals. Using the Paralisa™, it is now possible to implement management systems to electively remove Map infected deer resulting in reduced environmental contamination and improved production and reproductive performances. While this approach can significantly reduce Johne's disease levels within a deer herd we do not claim that it can be used to eradicate Map infection. Diagnostics have also been used to identify susceptibility traits linked to genotype (breeds), phenotype (male vs female) and production.