A number of studies have evaluated the efficacy of the new fluoroquinolones for therapy of bacterial enteric diseases and for prevention of gram-negative sepsis in granulocytopenic patients. The success of the quinolones in these settings is related to several special features of these agents, including their spectrum of activity and high fecal levels, which are in turn reflected in their effect on the gastrointestinal flora. Other factors that are important, particularly for invasive disease such as typhoid fever and shigellosis, include good intracellular and bowel wall penetration, and lymph node and systemic drug concentrations many times higher than the MICs of the causative organisms. This article reviews the factors that contribute to the changes in fecal flora, and the results of clinical studies in patients with diarrhea, granulocytopenic patients, and patients with selected other infections of, or related to, the gastrointestinal tract.