The intestinal microbiota, a complex and dynamic population of different bacterial species, under normal circumstances, represents an important contribution to the health of the host. This plays a key role by maintaining the integrity of the epithelial barrier and helping the development of mucosal immunity. However, under some stressful situations, such as after gastrointestinal surgery, infectious complications may be originated from the patient's own intestinal microbiota. This leads to the so called "gut origin of sepsis" hypothesis. On the other hand, under similar conditions, the supply of probiotics, the good bacteria, has been shown to be beneficial, despite few controversial results. Therefore, it is important to carefully assess the efficacy of probiotics in the prevention and treatment of complications in surgical patients, as well as to evaluate the safety of its use.