Similar to that of all mammals, the human gastrointestinal tract is colonized by 100 trillion bacteria shortly after birth. Remarkably, in the open-tube arrangement of the intestine, this bacterial population is tightly compartmentalized to the distal gut. Contamination of the small intestine with colonic bacterial flora or small intestinal bacterial overgrowth (SIBO) has been understood previously as a complication of uncommon conditions associated with obvious intestinal stasis. However, SIBO has also been found in 78% to 84% of patients with the common condition of irritable bowel syndrome (IBS). In this paper, the diagnostic and treatment approaches to SIBO are reconsidered within the larger framework of the patient with IBS.