There is a range of pathology that can be seen in infected goats. Grossly (when the gastrointestinal tract is examined at necropsy), there can be a complete lack of lesions - the intestine may appear entirely normal. In cases at the other extreme, the intestine appears thickened and corrugated and the neighboring lymph nodes are enlarged and edematous. This thickening and enlargement is due to the influx of inflammatory cells to the infected region. These animals are often emaciated with a total lack of abdominal fat stores. The majority of cases fall between these two extremes. Animals with Johne’s disease die because their gastrointestinal tracts no longer can absorb and process the food they eat.

When the tissues are examined microscopically, again the animal may present one of a number of pathologic pictures for both clinically and sub-clinically affected goats. The tissues may appear normal in virtually every site. In other cases florid signs of infection such as numerous macrophages and giant cells packed with acid-fast rods may be present. Other cases may fall between these two extremes. The likely sites of infection are the terminal ileum and mesenteric lymph nodes although neighboring portions of the gastrointestinal tract (colon, jejunum) are frequently affected as well.

	Over the course of the disease, the extent of the tissue damage done by M. paratuberculosis varies. In early phases, no lesions may be detectable. In more advanced stages, lesions are found primarily in the gastrointestinal tract. The ileum may be thickened and corrugated and the neighboring lymph nodes are enlarged. Indications of the infection may be found through microscopic examination of the ileum or lymph nodes even if no signs are visible with the unaided eye.

Thickened intestinal mucosa due to Johne's disease.