OBJECTIVE To determine whether fecal bacteriotherapy results in a durable beneficial change in the colonic microbiota of patients with flora-related disorders. BACKGROUND Earlier studies have implicated the colonic microbiota in a number of conditions. Administration of a fecal suspension from a healthy individual to an ill individual (fecal bacteriotherapy) can cure Clostridium difficile infection and potentially other diseases. Oral probiotics do not work in this condition, yet there has been no study to determine whether fecal bacteriotherapy results in prolonged implantation. METHODS Fecal samples were collected from 10 patients undergoing fecal bacteriotherapy. Patients completed an antibiotic schedule and bowel lavage before the infusion of healthy donor feces. Using a molecular approach, the bacterial populations in patient fecal samples were followed from pretreatment to 24 weeks post-initial infusion and compared with the initial infused donor fecal suspension. RESULTS At intervals of 4, 8, and 24 weeks after the procedure, the bacterial populations in the patients' fecal samples consisted predominantly of bacteria derived from the healthy donor samples. Comparisons of similarity at 4, 8, and 24 week samples to the donor-infused sample were made and each recipient's baseline sample was statistically significant with Friedman test. CONCLUSIONS This study demonstrates a durable beneficial change in the patients' bacterial populations of the colon to represent those of the healthy donor's microbiota. Manipulation of the colonic microbiota to improve its protective and beneficial role represents a promising field of new therapeutic strategies for the treatment of gastrointestinal conditions.