Bovine Paratuberculosis is a chronic, debilitating disease resulting in huge economic losses to the dairy industry. The present study was conducted to determine the frequency of Paratuberculosis infection in cattle and buffaloes slaughtered at Faisalabad abattoir, Pakistan. The study carried out on a total of 400 animals including cattle (200) and buffaloes (200). On the basis of PCR, 0.5% buffaloes and 1.5% cattle were found positive for Paratuberculosis. From 25 cattle and 20 buffaloes the suspected morbid samples of intestine and mesenteric lymph nodes were collected and were further processed for histopathology analysis and molecular characterization using polymerase chain reaction techniques (PCR). A total of 18 cases of intestine showed haemorrahages, out of these 2 cases showed thickened mucosa and corrugation. These samples were further processed for histopathology and PCR. The results revealed that out of 45 morbid samples (25 cattle + 20 buffaloes), 4 were confirmed by PCR for Mycobacterium Paratuberculosis. The histopathology examination of intestine tissues revealed diffuse inflammatory reaction, mononuclear cell infiltration along with degenerative and necrotic changes in sub-mucosal glands of the intestine. The immature granuloma formation was also observed in both intestine and lymph nodes.The study concluded that the disease was prevalent (1%) in animals coming for slaughtering at Faisalabad abattoir.