The gastrointestinal tract, and the colon in particular, is host to a number of bacteria that reside within its lumen. In health, greater than 90% of this flora is composed of anaerobes, whereas facultative anaerobes and aerobes are present in smaller numbers. The recent development of molecular methods to quantify these bacteria provides powerful tools to study the influence of these organisms on bowel function. These studies indicate that about 75% of fecal bacteria can be characterized, and belong to the 3 dominant groups—the Clostridium coccoides-Eubacterium rectale group, Clostridium leptum group, and Bacteroides-Prevotella group. The development and maturation of the enteric flora, and also the diversity of the flora, is reviewed. Multiple factors regulate the population number of these bacteria, including gastric acidity, intestinal transit, dietary factors, antibiotic use, and bacterial interactions with other bacteria and with the epithelium. Anaerobic bacteria in the intestine change the redox status of the colon; they also produce molecules such as short chain fatty acids, which influence colonic epithelial and mucosal physiology in many ways. New knowledge suggests that these bacteria exert effects on host immunity, which extend well beyond the intestine.