Thrombosis in the right atrium or ventricle is a rare complication of permanent endocardial pacing in adults. To the best of our knowledge, this complication has not been previously reported at all in the pediatric age group. We report on a case of a 7-year-old boy who had large left ventricular thrombi that occurred during permanent endocardial electrical stimulation. Subsequent pulmonary emboli complicated congestive heart failure in this patient. As a diagnostic approach, echocardiography and pulmonary perfusion scintigraphy were used. We comment on possible causes of this serious complication and suggest hemorrheological and platelet activation studies in patients with permanent endocardial pacing.