Surgical site infections (SSIs), such as wound infection, fascial dehiscence, and intraabdominal abscess, commonly occur following penetrating abdominal trauma. However, most of the literature involves penetrating colon injuries. There are few reports describing complications following penetrating stomach and small bowel injuries. Based on the hypothesis that SSIs are commonly found following penetrating stomach and small bowel trauma, a prospective observational study was performed at an academic Level I trauma center from March 1, 2004 until August 31, 2006. The subjects were patients who had sustained a penetrating injury to the stomach or small bowel. Patients were followed for the development of an SSI, defined as wound infection, fascial dehiscence, or intraabdominal abscess. A total of 178 patients were admitted with penetrating stomach or small bowel injuries over the 29-month period. There were 121 (68%) gunshot injuries and 57 (32%) stab wounds. Associated intraabdominal injuries occurred in 74% of patients. Overall, SSIs occurred in 20% of cases. Risk factors for SSI included associated duodenal or colon injury, whereas time to operating room, blood loss, and type and duration of antibiotic use were not. When associated colon injuries were excluded, SSIs occurred in 16% of patients with gastric injuries and 13% of those with small bowel injuries. SSIs commonly follow penetrating stomach and small bowel trauma. Risk factors for SSI include associated duodenal or colon injury. Delay to operating room, blood loss, and type and length of antibiotic prophylaxis were not associated with an increased risk of SSI.