Autologous Stem Cell Transplant for Crohn's Disease

Inclusion Criteria: * Diagnosis of Crohn's disease by standard criteria * Active disease based on clinical symptoms, defined as CDAI \>250. In patients with an ostomy, the number of liquid stools score in the CDAI will be replaced by the number of times that the ostomy bag is emptied daily. * Active disease based on endoscopic evaluation, defined as SES-CD score \> 3 in at least one bowel segment * Failure to respond to (or intolerant/adverse reaction to or declines) a member of each of the class of drugs listed below: 1. corticosteroids 2. azathioprine, 3. 6-mercaptopurine, methotrexate 4. Anti-TNFα (infliximab, adalimumab, certolizumab, golimumab) 5. Anti-integrin agents (natalizumab, vedolizumab) 6. Ustekinumab * Failure to respond refers to ongoing objective inflammation with symptoms and, as is traditional, is defined by the gastroenterologist evaluating the patient. * No surgical therapeutic option secondary to risk of short bowel syndrome or patient refusal Exclusion Criteria: * History of significant toxicity to any medications used in trial (cyclophosphamide, thymoglobulin, vedolizumab) * Pregnant or breastfeeding * Age \<18 * Karnofsky Performance Score \<60 * Patients who have an uncontrolled infection (presumed or documented) despite appropriate therapy for at least one month * Patients with symptomatic coronary artery disease or uncontrolled congestive heart failure. * HIV infected * Ejection fraction \<30% or requiring supplemental continuous oxygen. * DLCO \<35% or requiring supplementary oxygen. * Patients for whom an insufficient number of stem cells (\<2 X 10\^6/kg) have been collected.