The majority of patients with Crohn's disease (CD) require surgery during the course of their disease, but such surgery is typically not curative. Although some studies suggest that the disease state is theoretically reset to its earliest phase following surgery, disease phenotype and natural history of CD do not change significantly after surgery, leading to high rates of recurrence. Factors predisposing to this recurrence are not well defined, so there is a need for and a unique opportunity to develop a better understanding of the pathogenesis of recurrent inflammation and associated risk factors after an ileocolic resection. This paper reviews the postoperative disease outcome and evolution based on defining the combination of the patient's microbial flora, environmental exposure history, immune response and genetic make-up.