Inflammatory Bowel Disease (IBD) comprises Crohn's Disease (CD), ulcerative colitis and undetermined colitis which is becoming a major health problem in developed societies reaching higher levels of affected patients each year. Although the etiology of CD is not clear and it has been believed to be an autoimmune disease, its similarity in symptoms to paratuberculosis and the isolation of Mycobacterium avium subsp. paratuberculosis (Map) from gut, lymphoid tissue and blood of CD patients suggests that Map could play an important role in this illness. Our aim was to confirm the presence of Map in the bloodstream of IBD patients from Gipuzkoa in the Basque Country. A blind assay that included DNA extraction of buffy coat and nested PCR for the amplification of IS900 from 65 patients as well as 101 healthy controls was performed. We found that 41.5% of IBD patients were positive to IS900, whereas 42.5% of the controls presented IS900. These results do not show any association of Map with IBD, but are in agreement with those of Naser et al. (2004) indicating a strikingly high frequency of Map carriers among healthy individuals. Similar findings have been done in cattle, where Map DNA can be found in blood of animals both in affected and unaffected herds. This observation suggests that development of disease caused by Map might be strongly influenced by genetic and/or environmental factors. Among the former, mutations in NOD2, a gene that codifies for a receptor of lipopolysacharides have shown to have a strong association with CD. The detection of Map in blood along with NOD2 analysis of CD patients and ruminants should be considered in future studies in order to clarify the role of Map in CD.