Paratuberculosis, a disease caused by Mycobacterium paratuberculosis is a peril for both livestock and human beings. The present project was designed to study the pathmorphological changes induced by the organism and standardize more reliable diagnostic techniques to identify the M paratuberculosis. Tissue samples from ileurn and mesenteric lymph nodes were randomly collected from 1 50 cattle and buffalo, each in present study that was conducted in Lahore.

Gross lesions were recorded on a Performa. The samples were subjected to acid fast staining of smears from pellets after density gradient centrifugation and paraffin embedded tissue sections. All the samples also subjected to polymerase chain reaction and immunohistochemistry. The smears prepared from bacterial pellets of mucosal and cortical scraping of terminal ileum and MLN were stained indicated 11.4 % small intestine and 12.7% lymph nodes of cattle's and 8.7% and 10.7% lymph nodes of buffalo's tissue samples were positive. ZN staining of paraffin embedded tissue showed 8.0 % small intestine and 10% MLN of cattle's and 6.0 % of small intestine and 8.7% MLN in buffalo's tissue samples were positive. On basis of PCR 5.4% intestinal tissue samples and 6.0% MLN of cattle were positive. 3.4% intestinal tissue samples and 07(4.7%) MLN of buffaloes were positive. In buffaloes 4.0% intestinal tissue samples and 6.0% MLN were positive by IHC. In cattle 6.7% intestinal tissue samples and 8.0% MLN tissue samples were positive by IHC. In cattle, 27/150(18.0%) animals showed lesions in both intestine and mesenteric lymph nodes while 5/32 (15.7%) animals showed lesions in lymph nodes only. Out of 27/150(18.0%) intestinal tissue samples, 20/27 (74.1%) samples showed corrugation of the intestinal mucosa while 7/27 (26%) showed diffuse thickness.

In buffalo, 24/150 (16.0%) animals showed lesion in both intestine and mesenteric lymph nodes while 2/26 (7.7%) animals showed lesion in lymph nodes only. Out of 24 intestinal tissue samples, 19/24(79.2%) with gross lesion, samples showed corrugation of the intestinal mucosa while 5/24(20.9%) showed diffuse thickness.

In histopathology 20/27 samples of cattle showed focal granulomatous lesions while 7/27(26%) samples showed sever infiltration of macrophages and lymphocytes while 28/32(87.5%) lymph nodes showed infiltration of paracortical and cortical region of the lymph nodes with macrophages ,lymphocytes and multinucleated giant cells While 4/32 (12.5%) samples showed moderate infiltration of macrophages.

In buffaloes 19/24 (12.7%) samples showed focal granulomatous lesions while 5/24 (20.9%) samples showed sever infiltration of macrophages and lymphocytes while 22/26 (84.7%) lymph nodes showed infiltration of paracortical and cortical region of the lymph nodes with macrophages ,lymphocytes and multinucleated giant cells While 4/26 (15.4%) samples showed moderate infiltration of macrophages.

The sensitivity and specificity of immunohistochemical method was found significant in comparison Ziehl-Neelsen staining and histopathology for the diagnosis of paratuberculosis in cattle and buffaloes.