Background: The administration of indometacin to rats increases intestinal permeability and induces inflammatory pathology of the small bowel. This represents a potential model for Crohn’s disease. Aims: To analyse the pathogenic role of T cells, tumour necrosis factor and bacterial flora in indometacin‐induced changes in small bowel permeability and inflammation. Methods: Rats were given indometacin, 13 mg/kg, on day 1 and day 2. The effects of antibiotic (metronidazole, aztreonam and amoxicillin/clavulanic acid), anti‐ tumour necrosis factor and interleukin‐10 therapy were evaluated. The parameters used were weight change, serum haemoglobin, chromium‐51 ethylenediaminetetra‐acetate permeability and macro‐and microscopic score on day 5. Results in conventionally harboured rats were compared with those in T‐cell‐free rats. Additional in vitro experiments were carried out to test the effect of metronidazole on tumour necrosis factor production. Results: Indometacin administration resulted in small bowel ulcers and inflammation, independently of T cells. Metronidazole was more potent than amoxicillin/clavulanic acid and anti‐tumour necrosis factor in improving the indometacin‐induced small bowel inflammation. Only part of the efficacy was through improvement of increased intestinal permeability. Aztreonam and interleukin‐10 had no effect. Metronidazole also suppressed in vitro lipopolysaccharide‐induced tumour necrosis factor production, suggesting a therapeutic effect of this drug through the inhibition of tumour necrosis factor. Conclusions: These data implicate anaerobic bacteria and tumour necrosis factor production, but not T cells, as essential elements of the pathogenesis of indometacin‐induced small bowel inflammation. Tumour necrosis factor is also involved in the change in intestinal permeability. Metronidazole was the most efficacious drug in this model, probably because it suppressed anaerobic bacteria and directly inhibited tumour necrosis factor production.