Ovine clinical paratuberculosis is characterized by a chronic granulomatous enteritis. Various forms of intestinal pathology have been reported possibly corresponding to the stage or level of the host immune response. As part of a wider program of investigation, diseased (24) and control (24) sheep have been necropsied and gross and histopathological assessments of intestinal and other tissue lesions have been made. In addition morphometric measurements of gut tissues have been performed using image analysis. Results demonstrate marked changes in the diseased group concerning mucosal thickness, villus atrophy, cellular infiltration, etc. Within the diseased group various subgroups are recognizable and relate particularly to infiltrating cell type and mycobacterial load. There is significant correlation between mycobacterial load and the type of cellular infiltration seen in the gut. However serological analysis is less clear cut with AGID positive results detected in many animals with various advanced lesions. Histopathological and morphometric analysis of intestinal lesions proves a data base for assessing possible correlations with further immunohistochemical and molecular investigations.