Background: While dysbiosis is known to occur in patients with Crohn’s disease, the implications in clinical practice have been thus far limited. Through the formation of an ileostomy, the contents of the faecal stream including bacteria and other antigenic substances travel through the terminal ileum without turbulence and without reflux of colonic bacterial species. In this systematic review, the impact of temporary ileostomy formation at the time of ileocolonic resection on the recurrence risk of Crohn’s disease has been evaluated. Methods: A systematic search of PubMed, Embase, Cochrane and Clinical Knowledge Network (CKN) was conducted to identify studies which compared the risk of recurrence of luminal Crohn’s disease in patients who have underwent ileocolonic resection with primary anastomosis versus patients who underwent ileocolonic resection with temporary ileostomy. Two independent reviewers selected studies based on eligibility criteria for full text review and assessed how recurrence outcomes were defined and how risk was measured. Results: The search of the literature resulted in 946 hits from which four articles were included for this systematic review. Recurrence was defined based on endoscopic findings in three papers, need for repeat surgical intervention in three papers, radiological findings in one paper, and clinical assessment in one paper. Recurrence risk was quantified using cumulative incidence in one paper and using survival analysis in three papers. Conclusion: This systematic review highlights the current dearth of research on the impact of an ileostomy on the risk of recurrence of Crohn’s disease in patients undergoing an ileocolonic resection. Further studies which adequately control for confounding are required.