Fecal microbiota transplantation (FMT) is highly effective for treating recurrent Clostridioides difficile infection (CDI), with emerging data on intermediate and long-term safety.A prospective survey-based study was conducted (9/2012-6/2018) in patients undergoing FMT for recurrent CDI. Data on demographics and comorbidities were abstracted from medical records. Patients were contacted at 1 week, 1 month, 6 months, 1 year (short-term), ≥2 years post-FMT (long-term). Symptoms and new medical diagnoses were recorded at each time point. Data were weighted to account for survey non-response bias. Multivariate logistic regression models for adverse events were built using age (per 10-year increment), sex, time of survey and comorbidities. P<0.05 was considered statistically significant.Overall, 609 patients underwent FMT; median age 56 years (range, 18-94), 64.8% were female, 22.8% had inflammatory bowel disease (IBD). At short-term follow up (n=609), >60% patients had diarrhea, <33% had constipation. At 1 year, 9.5% reported additional CDI episodes. On multivariable analysis, patients with IBD, dialysis dependent kidney disease and multiple FMTs had higher risk of diarrhea; risk of constipation was higher in females and lower in IBD (all p<0.05). For long-term follow up (n=447), median time of follow up was 3.7 years (range, 2.0-6.8). Overall, 73 new diagnoses were reported- 13% gastrointestinal, 10% weight gain, 11.8% new infections (all deemed unrelated to FMT). Median time to infections was 29 months (range, 0-73) post-FMT.FMT appears safe with low risk of transmission of infections. Several new diagnoses were reported, which should be explored in future studies.