Inflammatory bowel disease (IBD) comprises a spectrum of chronic inflammatory disorders whose precise aetiology remains elusive, although genetic, immunological and psychic factors are known to play a pathogenic role. Standard medical therapy includes corticosteroid in the acute phase, mesalazine or immunomodulants to maintain remission and biological agents for refractory and/or severe cases. Since the precise causation of IBD remains unclear, treatment is currently aimed at treating symptoms or, at best, general rather than specific pathophysiological changes, which accounts for the sometimes mediocre and unsatisfactory results often observed in clinical practice. Moreover, most of the drugs currently employed to treat IBD exert untoward effects, especially during long-term treatment. Recently a body of evidence has suggested a distinct role of enteric microbial flora in inducing and maintaining intestinal inflammation through a complex interplay with the gut immune system. Accordingly, certain antibiotics such as metronidazole and ciprofloxacin have been successfully employed, especially in Crohn's disease [1]. In view of the side-effects of prolonged administration of systemic antibiotics, rifaximin, a poorly absorbed, locally acting antibacterial agent, has also been tested, with promising results [1]. A safer and even more attractive therapeutic alternative is offered by probiotics, with or without the addition of prebiotics, a ‘natural’ approach to IBD treatment. In this issue of the Journal, Damaskos and Kolios [2] provide an exhaustive and interesting overview of the role of alterations in intestinal microflora (so-called dysbiosis) in IBD and the possible therapeutic effect of probiotics in restoring the balance, thus reducing or preventing intestinal inflammation. What is clear from the available clinical data and needs to be emphasized is the concept that probiotics, far from being all alike, exhibit profound differences in their mechanisms of action and therefore in their therapeutic effects, even within the same genre. Another important observation is that the observations carried out in experimental models do not necessarily predict what will actually take place in clinical practice. For example, Lactobacillus strains were found to attenuate colitis induced by various agents, but in the clinical setting proved to be ineffective in preventing relapse of Crohn's disease in both adults and children [3–5]. In contrast, the yeast Saccharomyces boulardii, when added to mesalazine, has been shown to maintain remission of inactive Crohn's disease more effectively than mesalazine alone [6]. On the other hand, the probiotic mixture named VSL #3, although sometimes providing disappointing results in experimental models, has been shown in several clinical trials to prevent recurrence of pouchitis [2]. On the whole, it appears that each single probiotic agent has to be separately tested in clinical practice, time-consuming and irritating though this process can be. As for prebiotics, the scenario is even more confusing due to the scarcity of well-performed clinical studies. Hence it is almost impossible to draw definite conclusions about the potential role of combinations of pro- and prebiotics (synbiotics) in intestinal disorders as a whole and in IBD in particular. As aptly observed by Damaskos and Kolios [2], mixtures expected to act synergistically might fail to exhibit the predicted results, and so many combinations of probiotics and prebiotics can be postulated that the number of trials to be performed is overwhelming. In conclusion, there is a sound rationale for the use of probiotics in the treatment of IBD. From the published studies some probiotics (S. boulardii, VSL #3) appear to be clinically effective, whereas others either do not offer any substantial benefit or are still to be evaluated in controlled trials. Prebiotics can enhance the efficacy of probiotics alone, but the quality and quantity of the studies available so far are too limited to identify the most effective synbiotic combinations.