For the treatment of refractory Crohn’s disease (CD) autologous stem cell transplant (auto-SCT) is unparalleled in its ability to induce clinical and endoscopic remission.(1, 2) Auto-SCT is unique as a cellular therapy aimed to reset immune pathophysiology to a pre-disease state using hematopoietic stem cells. As such, the study of how the immune system responds to auto-SCT will provide unique insight into CD pathogenesis and treatment. To date, no studies in any cohort have defined the mucosal and peripheral immune response to auto-SCT.