BACKGROUND & AIMS: Adherent-invasive Escherichia coli (AIEC) pathovar has been identified in the intestinal mucosa of patients with Crohn's disease (CD). AIEC reference strain LF82 is able to adhere to intestinal epithelial cells, to invade epithelial cells via a mechanism involving actin polymerization and microtubules, and to survive and replicate within macrophages. This study was performed to assess the prevalence of AIEC associated with intestinal mucosa of patients with CD, ulcerative colitis (UC), and of controls. METHODS: A search for E. coli strains was performed with ileal specimens of 63 patients with CD and 16 controls without inflammatory bowel disease (IBD), and with colonic specimens of 27 patients with CD, 8 patients with UC, and 102 controls. The abilities of E. coli strains to invade epithelial cells and to survive and replicate within macrophages were assessed using the gentamicin protection assay. Bacterial uptake by epithelial cells was analyzed using cytoskeletal inhibitors. Bacterial adhesion was quantified with Caco-2 and Intestine-407 cells. The presence of known E. coli virulence genes was assessed by polymerase chain reaction and DNA hybridization. RESULTS: In ileal specimens, AIEC strains were found in 21.7% of CD chronic lesions vs. in 6.2% of controls. In neoterminal ileal specimens, AIEC strains were found in 36.4% of CD early lesions (P = 0.034 vs. controls) and 22.2% of healthy mucosa of CD patients. In colonic specimens, AIEC strains were found in 3.7% of CD patients, 0% of UC patients, and 1.9% of controls. CONCLUSIONS: AIEC strains are associated specifically with ileal mucosa in CD.