This study analyzed 28 thrombotic children with various cardiac disorders. They comprise 17% of a total of 168 patients with thrombosis from a single center. Among the 28 patients, 21 had congenital heart disease and 7 were diagnosed with cardiomyopathy. The patients with thrombosis were evaluated for congenital and acquired thrombotic risk factors. In addition to cardiac disorders, two, three, or more risk factors were present in 61% of the children with thrombosis. Two common mutations, namely factor V Leiden and prothrombin G20210A mutations, were found in 6 patients (22%). Nine patients (32%) died of infection, congenital heart disease, cardiomyopathy, thrombosis, operation, or a combination of these; two patients required surgical intervention. Following cardiac angiography, due to necrosis, amputation of the right index finger and right lower extremity was performed on 1 patient. The second patient's index fingers had to be amputated and resection of the bowel was performed following the operation on coarctation of the aorta. This study indicates that congenital heart disease and cardiomyopathy are two common cardiac disorders that may lead to the development of thrombosis. The majority of thrombosis develops within the heart and/or its great vessels. The second predominant site for thromboembolic symptoms is in the brain, including sinovenous thrombosis.