Factor V Leiden mutation is reportedly the most common hereditary risk factor for thrombosis. Spontaneous venous thromboses in children with factor V Leiden are rare without the presence of an additional risk factor for thrombosis. Spontaneous arterial thromboses are even more rare. In this case report, we describe an unusual case of a neonate born with both arterial and venous thromboses involving the left brachial artery, the left brachial vein, and stroke involving the right middle cerebral artery. The infant was subsequently found to be heterozygous for the factor V Leiden mutation. His mother was also heterozygous for the mutation but did not have a history of thrombosis. Evaluation for the factor V Leiden mutation should form part of the work-up of an infant with either arterial or venous thromboses or stroke because it increases the infant's relative risk for future thrombosis.