Thrombosis of the aorta in the neonate is a potentially catastrophic event. The incidence of this problem has increased concomitantly with the widespread use of umbilical artery catheters in the management of infants who are critically ill. The natural history and appropriate management of this complication has not been well established. This is due in part to the wide spectrum of presentations and lack of consensus regarding its classification. Aortic thrombosis may vary from deposition of a fibrin sheath surrounding the length of an umbilical artery catheter to aggregates of nonocclusive thrombus within the aorta or to complete occlusion of the aorta and concomitant occlusion of its main branches. The reported treatments recommended for this problem have ranged from supportive care only to mandatory surgical intervention in all cases. This spectrum of advocated therapies has resulted in considerable confusion regarding the proper management of this problem. This paper presents two cases of neonatal aortic thrombosis: one case was treated medically and the other case was treated with surgical intervention. We review these cases and the current literature, with specific attention directed towards highlighting the critical elements involved in formulating a reasonable approach to the management of neonatal aortic thrombosis. In addition, we offer an algorithm for management of these patients according to the degree of aortic thrombosis, severity of systemic manifestations, and the general condition of each individual patient.