Inflammatory bowel diseases are the result of an abnormal immune response to environmental factors including the intestinal microbiota. Epithelial and immune cells of the intestinal mucosa recognise specific bacterial molecules via Toll like and NOD like receptors and this interaction modulates the inflammatory response (activation of the NF-kappaB pathway). It is thus rational to try treatments which could modify the intestinal microbiota i.e. antibiotics, new substrates (prebiotics) or new micro-organisms (probiotics). We review the literature on existing evidence for the efficacy of probiotic strains or combinations in patients with pouchitis (good evidence), ulcerative colitis (fair evidence), and Crohn's disease (no evidence at the present time). We also discuss the mechanisms of action, the use of microbial agents as pharmacological vectors, the development of genetically modified probiotics (including a clinical pilot trial in patients with Crohn's disease), and safety issues.