The rationale for fecal microbiota transplantation in patients with refractory Clostridium difficile and/or Ulcerative Colitis or indeterminate colitis is its ability to reconstitute the normal microbial homeostasis leading to resolution or improvement of symptoms caused by the bacteria or underlying inflammatory bowel disease. This is becoming an especially important treatment modality as antimicrobial therapy for Clostridium difficile is becoming less efficacious due to resistant strains such as the hypervirulent NAP1/ribotype 027 strain.