An increasing amount of evidence suggests that enteric flora may have a role in the pathogenesis of inflammatory bowel disease (IBD). Patients with IBD appear to have an altered composition of luminal bacteria that may provide the stimulus for the chronic inflammation characterizing IBD. The suspected role of bacteria in the pathogenesis of IBD provides the rationale for using agents, such as antibiotics, that alter the intestinal flora. However, there remains much uncertainty about the optimal use of antibiotics in the treatment of Crohn's disease, ulcerative colitis, and pouchitis. This article reviews the literature and presents a clinical model for the use of antibiotics in IBD.