The United States Food and Drug Administration (FDA) exercises enforcement discretion for fecal microbiota transplantation (FMT) for Clostridium difficile infection not responsive to standard therapies. An investigational new drug (IND) is required for all other uses. Since enforcement discretion took effect in 2013, patients with Crohn’s disease (CD) and ulcerative colitis (UC) have enrolled in multiple trials as they are at an increased risk of Clostridium difficile infection. Trials of FMT to treat the inflammatory bowel disease (IBD) directly, independent of the impact on Clostridium difficile infection, are of particular interest to patients.