OBJECTIVE: Bacterial agents have been implicated in the early recurrence of Crohn's disease after ileocolectomy. The aim of our study was to identify and quantify bacteria associated with the ileal mucosa in patients and controls and to correlate specific bacteria with recurrence. METHODS: The predominant bacterial microflora of the ileum were enumerated and identified, aerobically and anaerobically, in biopsies obtained at the time of surgery or by endoscopy from 61 patients with Crohn's disease and 10 ileocolectomy controls. The 61 specimens were comprised of 13 ileal biopsies taken from resection specimens, seven taken after ileostomy, and 41 taken after ileocolectomy. RESULTS: Ileocolectomy induced a significant increase in bacterial counts and variety in the neoterminal ileum in both patients and controls that was not observed in ileostomy biopsies. Comparison between patients and controls revealed greater numbers of Escherichia coli and enterococci in Crohn's disease and of bifidobacteria and ruminococci in controls. Early recurrence was associated with high counts of E. coli and bacteroides and the frequent isolation of fusobacteria. CONCLUSION: After ileocolectomy, colonization of the neoterminal ileum is increased. Our data suggest that increases in the populations of specific bacteria such as E. coli, enterococci, bacteroides, and fusobacteria may be important in postoperative recurrence of Crohn's disease.