Of the 488 pediatric patients with thrombosis in a single center, 50 (10.2%) had nonstroke arterial thrombosis. Half of the nonstroke arterial thrombosis patients had a preceding arterial catheterization history. Infection was a common contributing underlying disorder among both catheterized and overall groups (28 and 42%, respectively). The third most common underlying risk factor for development of arterial thrombosis was associated cardiac disease, and 70% of these patients had congenital heart disease and 30% had dilated cardiomyopathy. The most common site of arterial thrombosis was the heart, and 22% of the patients developed arterial thrombosis following cardiac surgery for congenital heart diseases. The prothrombotic risk factors were also analyzed in the study group and factor V G1691A and PT G20210A heterozygous mutations were detected to be higher (16 and 4%, respectively) than those in healthy controls (7.4 and 2.3%, respectively). In addition to factor V G1691A and PT G20210A mutations, other prothrombotic risk factors including protein C and protein S deficiencies and elevated factor VIII levels were commonly associated with pediatric nonstroke arterial thrombosis cases in the present study. This finding indicates the importance of these factors in arterial thrombosis development, similar to venous thrombosis. Another striking factor of the study is the higher number of prothrombotic risk factors (more than three) in patients who had persistent thrombosis, indicating the need for more intensive treatment in these patients.