John'es disease is a chronic enteropathy of ruminants cause by infection with M. a. paratuberculosis. This study deals with the enumeration of Australian ovine isolates of M. a. paratuberculosis which will help facilitate research into the pathogenesis and epidemiology of OJD. It also covers the early detection of infection in lambs exposed to Australian ovine strains of M. a. paratuberculosis. Examination of sheep at this early stage, in particular the use of culture from tissues, allowed assessment of the current diagnostic techniques for detection of early infection in sheep and some investigation of early immune responses. The final chapter examines possible associations with host susceptibility to Johne's disease with polymorphisms in a number of genes associated with immune function