Johne’s Disease is a chronic, progressive intestinal disease caused by infection with Mycobacterium avium subspecies paratuberculosis (Map) that affects primarily ruminant animals. In recent decades there has been growing concern over the lack of effective control of this disease and questions have arisen regarding the possibility that Map infection could be a cause of some cases of Crohn’s disease in humans. This report presents a broad outline of the steps that should be taken to control Johne’s disease, reduce the spread of Map, and minimize effects of the disease in animals. The report also describes the weaknesses of current research agenda and provides recommendations for a new research strategy to resolve the question of whether there is a link between Johne’s and Crohn’s diseases.