The aim of this study was to determine the knowledge, compliance, and practice of antibiotic endocarditis prophylaxis (AEP) for patients with congenital heart disease (CHD) during various diagnostic or therapeutic procedures. Patients (296) and their parents were interrogated during a visit with an 18-question survey pertaining to the practice of AEP. Most patients (91.6%) had acyanotic congenital heart disease, usually preoperative (45.3%), or had high risk of infective endocarditis due to previous endocarditis (2.0%), cyanosis (8.4%), or prosthetic valves (5.4%). Potential sources for failure of AEP were (1) no existence of a wallet card (6.8%), no communication between patient and doctor concerning the potential risk of endocarditis during a visit (13.2%), or no sufficient anamnestic inquiry by the physician before procedures were performed (43.2%). The patients underestimated (4.4%) or had no knowledge of the individual risks of endocarditis (37.5%) or underestimated indication for AEP (11.1%). AEP was often not performed at all (60.5%). Bad dental status with no previous dental therapy (35.5%) and a high rate of caries (17.2%) or gingivitis (7.4%) even in young children was frequent. AEP for patients with CHD has not been sufficiently used because of the patient’s, and the physician’s failure to take the necessary steps, the cardiac diagnosis, or the dental health status. Alternative strategies in prophylaxis for AEP are discussed here.