Purpose: To determine the emergence of vancomycin-resistant enterococci (VRE) in stool after prophylactic intravenous treatment with vancomycin in patients undergoing surgery for congenital heart disease. Design: Prospective comparative study. Setting: Multidisciplinary and post-cardiac surgery pediatric intensive care units. Patients: Forty-one consecutive children aged 3 days to 18 years who underwent cardiac surgery and had not been treated with any antibiotics for 14 days prior to operation. All had positive stool cultures for enterococci. Eighteen children received only intravenous cefuroxime, 75 mg/kg/day for 2 days (control group), and 23 also received intravenous vancomycin, 30 mg/kg/day divided into 2 doses (study group). Intervention: Stool cultures for enterococci. Measurements and Results: Stool samples for bacterial culture were obtained before the antibiotic treatment, every day during the treatment, and 2 days after the drugs were discontinued. In cases of growth disappearance, cultures were taken until growth reappearance or discharge. In one of the 18 cefuroxime-treated children, fecal enterococcal growth disappeared one day after prophylactic treatment, and vancomycin-sensitive enterococci reappeared on the third day. In 5 of 23 vancomycin-prophylactic treated children, enterococcal growth disappeared after the second dose of vancomycin. The stool cultures then became positive for vancomycin-sensitive enterococci in 3 of the children and positive for vancomycin-resistant enterococci in one. In the fifth child, findings remained negative. Conclusions: Perioperative prophylactic treatment with intravenous vancomycin in children undergoing surgical treatment for congenital heart disease does not seem to significantly increase fecal VRE when given over a short period.