Deer farming is now a well established industry in New Zealand with over 6,000 farms containing more than a million animals. The first case of paratuberculosis in these deer was recorded in 1985 and during the next six years a further 20 cases were confirmed by bacterial culture. In the 1990s there has been a steady increase in the number of cases of paratuberculosis in farmed deer. In 1995, Mycobacterium paratuberculosis was isolated from over 50 deer from more than 30 different farms. A feature of paratuberculosis in deer is lesions in mesenteric lymph nodes which macroscopically and microscopically are very similar to thoe caused by other members of the Mycobacterium avium complex and by Mycobacterium bovis. The diagnosis of paratuberculosis in deer is further complicated in some cases by the presence of strains of M. paratuberculosis which are extremely difficult to isolate by bacterial culture. To overcome these problems we have evaluated the use of polymerase chain reaction (PCR) tests using primers based on the DNA insertion element IS900. Different DNA extraction procedures have been evaluated in an attempt to develop a robust and sensitive test for routine use in a diagnostic laboratory. PCR tests have proved to be an accurate and reliable test on tissues containing microscopically-visible acid-fast organisms. However, PCR tests are still not able to reliably detect M. paratuberculosis in tissues containing very small numbers of bacilli.