Universally accepted indications for the use of antibiotics in bowel disease include treatment of septic complications such as abscesses, bacterial overgrowth and toxic megacolon. The role of antibiotics as primary or secondary therapeutic agents for active intestinal inflammation is more controversial. Tetracycline, trimethoprim-sulphamethoxazole and ampicillin are used empirically by some experienced clinicians as alternatives to corticosteroids in patients with Crohn's disease but have not been subjected to well designed clinical trials. Only anecdotal reports suggest a benefit of broad spectrum antibiotics and bowel decontamination in patients with active ulcerative colitis. However, metronidazole (10 mg/kg) is equal to sulphasalazine and superior to placebo in well designed studies of patients with active Crohn's disease, with a particular benefit to those patients with colonic involvement. High dose metronidazole (20 mg/kg) is widely used for perianal complications of Crohn's disease, although its utility has never been documented by controlled trials. Reduction of luminal bacterial concentrations by intestinal lavage and nonabsorbable antibiotics induces remissions of Crohn's disease in uncontrolled trials but have not been used clinically. Long term use of antibiotics is tempered by the risk of complications, notably Clostridium difficile toxin-induced colitis with broad spectrum antibiotics and peripheral neuropathy after high dose metronidazole. The author advocates use of metronidazole 250 mg tid or qid (10 mg/kg) in patients with Crohn's colitis or ileocolitis who do not respond to sulphasalazine or 5-ASA, and treatment of perianal complications of Crohn's disease with metronidazole 500 mg tid (20 mg/kg), with immediate cessation of the drug if peripheral neuropathy occurs.