The effect of rifaximin on the intestinal bacterial population was studied in a clinical trial. Twelve patients with ulcerative colitis were administered rifaximin 1800 mg/day in 3 treatment periods of 10 days, each followed by 25 days of wash-out. Fecal samples were collected at the beginning and at the end of each treatment period to perform microbiological examinations. Titer variations of enterococci, coliforms, lactobacilli, bifidobacteria, Bacteroides spp., and Clostridium perfringens as well as their susceptibility to rifaximin during the different phases of the study were evaluated. The presence of Candida spp. was also monitored. After each wash-out period, concentrations of the intestinal microbial groups tested returned to initial values, showing that the administration of high doses of rifaximin does not significantly modify the colonic microbiota. Rifaximin-resistant isolates were also found, particularly in bacteria belonging to Bifidobacterium genus, included as probiotics in several fermented foods and in pharmaceutical preparations.