© 2016 AGA Institute Background & Aims Treatment of Crohn's disease (CD) may require multiple bowel resections that lead to short bowel syndrome. Intestinal transplantation is an effective treatment for short bowel syndrome, but limited data are available on long-term outcomes in CD. We aimed to characterize the long-term risk of rejection, graft failure, and death among patients with CD after intestinal transplantation, and compare their outcomes with those of patients without CD. Methods We performed a retrospective study of adults in the Scientific Registry of Transplant Recipients who received intestinal transplants in the United States from May 1990 through June 2014. Outcomes data were collected at 3 months, 6 months, 1 year, and every year after the procedure. We compared risks of rejection at 1 year after transplantation between patients with and without CD using the chi-square test and logistic regression. Longitudinal risks of graft failure and death were compared between patients with and without CD using the Kaplan-Meier method and Cox proportional hazards. Multivariable analyses adjusted for recipient, donor, and institutional characteristics. Results Of 1115 cases of intestinal transplantation, 142 were performed for CD and 973 for non-CD indications. One year after the procedure, the transplant was rejected in 36.9% of patients with CD and 33.3% of patients without CD (P =.48). For patients with CD, the actuarial risk of graft failure at 1, 5, and 10 years after intestinal transplantation was 18.6%, 38.7%, and 49.2%; the risk of death was 22.5%, 50.3%, and 59.7%, respectively. The risk of graft failure was greater for patients with CD (adjusted hazard ratio [aHR], 1.48; 95% CI, 1.03–2.13; P =.04), but patients with versus without CD had similar risks of death (aHR, 0.88; 95% CI, 0.64–1.20; P =.41). In subgroup analyses, the risk of graft failure was increased among patients with CD undergoing transplantation between 1990 and 2000 (aHR, 3.49; 95% CI, 1.23–9.92; P =.02), but not after 2000 (aHR, 1.37; 95% CI, 0.92–2.04; P =.12). Conclusions In an analysis of patients who received intestinal transplants, the risks of graft rejection or death were similar between patients with versus without CD. Before year 2000, patients with CD had an increased risk of graft failure, but not thereafter. Changes in posttransplant immunosuppression around the same time might be analyzed to learn more about the mechanisms and management strategies to reduce graft failure in CD.