Johne's disease in dairy cattle is a chronic infectious disease in the intestines caused by the baciili, Mycobacterium avium ssp. paratuberculosis. We have modeled this disease with several approaches to illustrate different features. A system of difference equations represented an epidemiological situation in dairy farm to compare the effects of two types of diagnostic tests. Then an agent-based model  at the farm level was developed to see the effects of stochasticity,   Lastly, a PDE/ODE model illustrated a novel way to link a within-host model with an epidemiological model.