M. avium subsp. paratuberculosis (Map) is the causative agent of Johne's Disease, a chronic granulomatous enteritis that affects adult cattle worldwide. It is one of the most prevalent and costly diseases of dairy cattle. Control methods to date have been limited due to the lack of sensitive diagnostic tests and methods to assess the potential efficacy of candidate vaccines. To facilitate analysis of the immune response to Map and candidate vaccines we developed a calf ileal cannulation model. An indwelling "T"-shaped, plastic cannula (0.5-1.0 inch ID), is surgically placed in the ileum with the sampling portal exiting the body wall at the right paralumbar fossa. Inflatable catheters are inserted into the intestinal lumen through the portal and run both oral and aboral to allow flushing, sampling and direct infection of an isolated segment of bowel. The model augments the establishment of experimental infections, monitoring the development of local and systemic immune responses, and the evaluation of disease progression in a step by step manor. Biopsies can be obtained for culture, RT-PCR, and histopathology. Importantly, the model provides a way to assess the capacity of candidate vaccines to elicit a protective immune response over a short time course. If protective immunity is elicited, impaired survival of challenge bacteria introduced into the ileum should be demonstrable. The ileal cannulation model augments in vitro methods of testing the immune response to candidate vaccines.