Faecal and organ examinations were carried out in 611 animals originating from eight paratuberculosis infected cattle herds. The diagnosis in the 479 cattle was set according to faecal (at least 3 months before slaughtering) and routine intestinal culture (ileum and the adjacent lymph nodes) after slaughtering. In the remaining 132 animals, post-mortem detailed culture was performed and samples were collected from the GIT (duodenum, jejunum, ileum, ileocaecal valve, caecum, rectum and the corresponding lymphnodes), lymphnodes (around the head, udder, lungs and liver), liver and spleen. In 251 (41.1%) of the animals, M.a.paratuberculosis could be isolated from the faeces; in 164 (65.7%) out of 251 shedding animals the infection was detected in the ileum and adjacent lymphnodes. The number of M.a.paratuberculosis present in organs of infected animals varied from 46.0% shedding 1 CFU, to 94.7% with massive shedding (correlation coefficient chi=0.79 and alpha=0.01). In 92 (25.5%) of the 360 non-shedding animals, the infection was culturally detected in the ileal mucosa and corresponding lymphnodes. Shedding animals had significantly higher (p=0.01) number of organisms in their organs than the non-shedding. During the detailed cultivation of other organs from 132 infected animals, 72 (54.5%) of them were positive. In 16.7%, the infection was spread in the intestine, parenchymatous organs, lymphnodes in lungs and head region and in 9.7% the infection was detected around the lymphnodes of the head region or the lungs. Randomly isolated strains were determined by DNA fingerprinting using IS900 as probe with restriction endonucleases Pstl and BstEII. Strains isolated from the faeces and organs of 150 infected animals were examined by DNA fingerprinting. Only six animals showed mixed infection caused by strains with different DNA types. Our research was partially supported by the Ministry of Agriculture of the Czech Republic (grant no. EP0960006087) and Czech Grant Agency (grants No. 514/95/1594 and 524/97/0948). Permanent address of Robin du Maine - Hogeschool van Utrecht, Netherlands.