Clostridium difficile infection (CDI) has emerged as a major complication associated with the use of systemic antimicrobial agents. Broad-spectrum antimicrobial agents disrupt the ecological bacterial balance in the colon and create an opportunity for C. difficile overgrowth with attendant production of toxins and clinical symptoms of colitis. Recommended therapies for CDI include oral administration of metronidazole or vancomycin for 10–14 days. However, 5% to 35% of patients experience infection relapse after completion of treatment. Recently, patients who failed to resolve their infection with conventional therapies and went on to develop chronic relapsing CDI were successfully treated with fecal bacteriotherapy. Stool obtained from a healthy individual was instilled from either end of the GI tract. Although the published experience with fecal bacteriotherapy is still limited, the published treatment results for 100 patients have demonstrated an average success-rate close to 90%. Fecal bacteriotherapy is a low tech procedure which is easy to perform, and breaks the cycles of repeated antibiotic use, which in turn reduces the risk of antibiotic associated resistance and adds potential cost savings when compared to repeated antibiotic administration and hospitalizations.