While a rationale for the use of probiotics can be developed for a number of functional gastrointestinal symptoms and syndromes and an experimental basis for their use continues to emerge, the only functional disorder for which an adequate database of clinical trials of probiotics to permit an assessment of clinical efficacy exists is the irritable bowel syndrome (IBS). IBS has also attracted attention, in this regard, because of recent revelations with regard to the potential roles of the enteric flora and immune activation in the pathogenesis of IBS, thereby, leading to a re-awakening of interest in bacteriotherapy in this common and challenging disorder. Some recent randomized controlled studies attest to the efficacy of some probiotics in alleviating individual IBS symptoms while selected strains have a more global impact. Evidence for long-term efficacy is also beginning to emerge though more studies are needed in this regard. Several other issues complicate the interpretation of much of the literature in this area: lack of quality control, use of many different species, and, strains and, above all, significant deficiencies in trial methodology.