Endocarditis is a potentially life-threatening disease in children with congenital heart disease (CHD) and correct prophylaxis (EP) is of utmost importance. We conducted two surveys among pediatricians and dentists in Flanders about their knowledge of EP guidelines. The survey was completed by 910 dentists and 100 pediatricians. Sixty-five percent of the dentists did not know any guideline. They relied for information on the internet or the child's physician. 87% identified low risk treatments correctly, but only 64% identified high risk procedures correctly. Eighty-three percent asked for the presence of CHD and allergy to antibiotics. Dentists asked advice of the patient's physician, but 29% would withhold treatments in high-risk patients and 50% did not know the pediatric antibiotic dosages. Forty-seven percent of the pediatricians did not know EP guidelines and they would preferably contact the child's cardiologist. Pediatricians had difficulties with the identification of low-risk procedures and would give unnecessary antibiotics. They identified most CHD at high risk, but scored lower for the identification of lower risk CHD. Conclusion: The knowledge of Flemish dentists and pediatricians of EP guidelines is low. The knowledge about EP guidelines and the communication between dentists and pediatricians should be improved. Patients should be provided with an individual EP card.