The purpose of this study was to describe the anatomopathological findings of three cases of paratuberculosis in autochthonous dairy cattle from Rio de Janeiro, Brazil. Animals presented characteristic clinical symptoms of paratuberculosis as cachexia, diarrhea and leanness, and were first diagnosed by sero-reactivity to an in-house ELISA. Animals were sacrificed and samples of small and large intestines, mesenteric lymph nodes and ileocaecal valve were collected and processed for both histopathology and bacteriology. Tissues were fixed in 10% buffered formalin, processed for paraffin inclusion and stained by both HE (haemathoxilin-eosin) and ZN (Ziehl-Neelsen) methods. Macroscopic alterations such as small intestine wall segmental thickness, mucosal hyperaemia and prominent corrugation were observed; ileocaecal valve emaciation, evident mesenteric lymphadenomegally, and lymphangiectasis were also noted. The main histopathological findings were enteritis, lymphangitis and granulomatous lymphadenitis. Intestinal lesions were mainly restricted to mucosa and submucosa of jejune and ileum, and characterised by inflammatory infiltration of lymphocytes, eosinophils, epithelioid macrophages and scarce giant Langhans-type cells. Numerous acid-fast bacilli were observed into macrophages, either alone or forming aggregates, on the top of villi, lamina propria and lymph nodes parenchyma. Most of the tissues yielded Map, and culture was confirmed by mycobactin dependence and specific PCR IS900. In conclusion, anatomopathology yielded characteristic findings that were later confirmed by culture and PCR. Therefore, due to its rapid results, low cost and reliability, this method (group of gross and microscopic lesions) was considered as a valuable tool for the diagnosis of paratuberculosis.