Background: Transient bacteremia after certain gastrointestinal endoscopies is well documented in adult patients; however, experience in pediatric patients is very limited. We conducted a prospective study to determine the frequency of bacteremia after common endoscopic procedures in children. Methods: A total of 108 endoscopies were performed in 95 patients (age range 8 months to 17 years; mean age 10.2 years). Procedures included 68 esophagogastroduodenoscopies (EGDs), 29 colonoscopies, and 11 flexible sigmoidoscopies. Most procedures (88) were performed with patients under conscious sedation; 20 were under general anesthesia with endotracheal intubation. Biopsy specimens were obtained from all patients. Blood samples for aerobic and anaerobic cultures were obtained prior to, and within 5 minutes of, completion of the procedure. In patients who underwent general anesthesia, a third sample was obtained 5 minutes after endotracheal intubation and before endoscopy. Results: Four of the pre-endoscopic blood cultures were positive. Two cultures were positive after endotracheal intubation, but were negative after endoscopy. Four cultures were positive after endoscopy. All organisms were skin or environmental flora and were considered contaminants. All patients with positive cultures remained asymptomatic during the 72 hours after the procedure. Conclusion: We conclude that clinically relevant bacteremia is very infrequent following routine endoscopic procedures with biopsies in immunocompetent children.