Growing evidence suggests a potential role of intestinal microbiota in irritable bowel syndrome (IBS) pathophysiology and symptom generation. Earlier studies based on classic microbiologic techniques hypothesized the presence of qualitative changes in intestinal microbiota in IBS patients. Recently, studies with molecular techniques have provided evidence of significant changes in microbial profiles in IBS and that the composition may be correlated with certain symptoms reported by patients. Although these studies are far from being exhaustive and conclusive they provide promising results that deserve further investigation. In addition, initial evidence indicated the presence of increased amounts of bacteria in the upper small intestine of IBS patients, a condition know as small intestinal bacterial overgrowth. However, the results of these studies have provided contradictory results suggesting that this area requires further work. These qualitative and quantitative changes in intestinal microbiota may induce different effects on the intestinal mucosa including mucosal barrier defects and immune activation which may contribute to symptom generation. Studies in IBS patients have attempted to target changes in intestinal microflora with different therapeutic approaches, such as the use of prebiotics, probiotics, synbiotics, and nonabsorbable and systemic antibiotics. Overall, the results obtained in probiotic clinical trials suggest some beneficial effect over placebo in the relief of IBS symptoms. However, these results, although encouraging, should be confirmed in larger well-designed, placebo-controlled studies. A number of open questions remain to be addressed, including the dose, type, and time of administration of probiotics.