Introduction: Fecal microbiota transplantation (FMT) has a 94% cure rate for recurrent C. difficile infection (CDI). Little is known about the efficacy and safety of FMT in patients with inflammatory bowel disease (IBD) and CDI. Methods: Cases with IBD and CDI treated with FMT via colonoscopy or sigmoidoscopy were retrospectively collected from 6 academic centers. Successful FMT was defined as resolution of diarrhea or negative stool C. difficile toxin. Results: Of 41 cases, 23 (56%) were females with median age of 47 years (range 21-81), 21 (51%) had Crohn’s disease (CD), 19 (46%) ulcerative colitis (UC), and 1 indeterminate colitis. CD involvement was ileal in 5%, colonic in 50%, ileocolonic in 43%; phenotype was inflammatory in 53%, stricturing in 24%, and penetrating in 23%. UC location was rectosigmoid in 11% and pancolonic in 89%. One month prior to FMT, 59% had active IBD and 41% were in clinical remission. Median HBI score was 7.5 (range 0-19), median UCCS score was 3.5 (range 1-10). Endoscopic disease activity at FMT was severe in 17%, moderate in 20%, mild in 46%, and quiescent in 17%. Twenty-six (63%) patients were considered immunosuppressed at the time of FMT. Of these, 8 were treated with a biologic agent, 7 with an immunomodulator, 3 with combination therapy, 2 with tacrolimus, and 14 with prednisone ≥20 mg/d. Indication for FMT was recurrent CDI in 83%, refractory in 10%, recurrent-refractory in 7%. Median number of CDI episodes was 4 (range 1-12). Median duration of CDI was 9.5 months (range 2-108). Twenty-six (54%) failed vancomycin taper. None had severe CDI. A single FMT was successful in 33 (80%) of patients. Three out of 4 patients were cured with a second FMT. The overall success rate of FMT was 90%. Of those who did not respond to the first FMT, 2 were immunocompromised. Three patients had CDI recurrence within 3 months after FMT. The clinical course of IBD within 3 months post FMT did not change in 14 (34%), improved in 20 (49%), and worsened in 7 (17%); median HBI score was 2 (range 0-15), UCCS score was 2 (range 0-3). Twelve patients were started on a new IBD medication. Six patients had SAEs requiring hospitalization: 1 underwent total proctocolectomy for refractory CD, 1 diverting ileostomy for refractory CDI, 1 for UC flare that responded to prednisone, 1 non-infectious severe diarrhea without endoscopically active IBD that responded to budesonide, and 1 for recurrent CDI and worsening CD in the ileal pouch that responded to vancomycin and adalimumab. Conclusion: FMT is effective for treatment of CDI in IBD patients; however, repeat FMT may be required to achieve >90% success rate. The course of IBD improved or did not change in the majority of patients. IBD worsened post-FMT in a significant minority of cases.