Infections, sepsis and multiple organ failure syndrome are associated with high morbidity and mortality in human and experimental small bowel transplantation (SBTx). These complications are attributed to bacterial translocation demonstrated in animal and human studies. Bacterial translocation (BT) is defined as the passage of viable bacteria from the intestinal lumen to other tissues or organs. BT has been associated with different clinical and experimental situations, hemorrhagic shock, trauma, bowel obstruction, immunodepression, total parenteral nutrition, antibiotics. Although BT has been investigated in several small and large animal models of SBTx, precise information on the mechanisms involved are not available. It is possible that the operative procedure by itself may promote BT for the interaction of a number of factors such as preservation, ischemia/reperfusion, abnormal motility, lymphatic disruption and aberrant systemic venous drainage, acute or chronic rejection and antibiotic therapy. Furthermore, the potent immunosuppressive therapy used in these patients may augment the deleterious effects caused by BT. In this review we examined the existing literature concerning BT with particular regard to intestinal transplantation, to better understand the alterations in the symbiotic relationship between immunocompromised host and his gut microflora after SBTx.