Crohn's disease is a chronic inflammatory disease of the gastro-intestinal tract, despite is first correlation with Mycobacterium avium subs. paratuberculosis since 1913, it is not yet established its role in Crohn's disease. In this study, we report the presence of cell wall deficient M. paratuberculosis in paraffin embedded tissue from patients with Crohn's disease by in situ hybridization. IS900 PCR was positive in 10% of tissues analyzed whereas Ziehl Neelsen stain was negative. We are currently trying to use policlonal and monoclonal antibodies to detect M. paratuberculosis within the same samples. These results suggest the possible use of in situ hybridization in the clinical practice to confirm the presence of M. paratuberculosis in Crohn's disease patients.