Ferrets (Mustela putorius furo) were released in New Zealand in the 19th century for the control of rabbits. Currently they inhabit large portions of the North and South Islands, especially those areas with moderate to high numbers of rabbits. Mycobacterium bovis was first isolated from wild ferrets in 1982 and they have been extensively studied to determine their role in the maintenance and spread of bovine tuberculosis. Recently, ferrets from the North and South Islands were identified with lesions in mesenteric lymph nodes and livers that contained acid-fast staining bacteria. The histological picture of these cases was not typical of that seen in ferrets infected with M. bovis and mycobacteria were not isolated from them using non-mycobactin, supplemented media. However, IS900 was detected in these lesions by PCR. Subsequently, M. paratuberculosis was isolated from these animals using Bactec vials supplemented with mycobactin, egg yolk and antibiotics. Characterisation of the isolates by Southern blotting using a DNA probe from IS900 showed that these isolates were the "ovine" subtype of M. paratuberculosis. Sources of infection for ferrets of the "ovine" subtype in New Zealand include sheep, farmed deer and possibly rabbits. While rabbits are known to carry M. paratuberculosis in some countries, in New Zealand they have not yet been examined for this organism. A wildlife reservoir of infection has major implications for the control of paratuberculosis.