Mycobacteria ingested by macrophages are able to inhibit phagosome maturation and phagosome lysosome fusion and the subsequent degradation of internalised material. The activation of macrophages and presentation of mycobacterial antigens to T-lymphocytes is important for the elimination of mycobacteria and is mainly mediated through the secretion of IFN-gamma. Mycobacteria can interfere with this process by affecting macrophage MHC expression. The aim of this study was to examine the histological and immune- and enzyme histochemical phenotypes of macrophages in the paratuberculosis lesions of goats experimentally infected with M. a. paratuberculosis. The granulomatous lesions in the small intestine of goats consisted of large macrophages with round to oval nuclei and abundant pale stained cytoplasm. These lesions were predominantly located in the lamina propria and submucosa of the intestinal wall. Few to many acid-fast bacilli were observed in the macrophages. The macrophages in these granulomatous lesions showed a low level of expression of MHC compared with macrophages in areas of the lamina propria without lesions. A further comparison of these two macrophage populations revealed low levels of expression of CD68, a marker for lysosomal membranes, and strong reactivity for acid phosphatase in macrophages of granulomatous lesions. The present study demonstrates clear phenotypic differences between macrophages in granulomatous lesions and in adjacent non-affected areas. These differences suggest that the functional status of macrophages is altered in mycobacterial lesions and may reflect inhibition of antigen presentation and changes in phagosome and lysosome function.