Irritable bowel syndrome (IBS) is a complex, yet common diagnosis in gastroenterology. Recent data suggest the increasing importance of bacteria in the pathophysiology of IBS. Some studies have shown that IBS can be precipitated by an acute case of gastroenteritis. These pathogenic organisms may contribute to long-term gut dysfunction. In another line of effort, a growing body of evidence links IBS to the presence of excessive bacteria in the small bowel, called bacterial overgrowth. Although the means by which this is determined have been indirect, studies demonstrating the benefit of unabsorbed antibiotics suggest that reduction in gut flora is important. Further work has also examined bacterial overgrowth in the context of the various symptoms of patients with IBS. These symptom complexes include constipation, diarrhea, and alternating forms of the condition. Although this idea seems initially counterintuitive, it has been demonstrated that the fermentation of methane in the gut is associated with and can result in the slowing of intestinal transit, resulting in constipation. In this review, these topics are discussed and outlined.