Intravascular and intracardiac clots, thrombi, and vegetative material can be safely and effectively treated with the AngioVac System (AngioDynamics, Latham, NY) as an alternative to open surgery. However, this technology is still not performed in children or adolescents as a rule. We aimed to present our experience with two cases (a 10 year old girl and a 17 year old male adolescent) with concurrent hypoxemia in whom this device was successfully used in combination with venovenous extracorporeal membrane oxygenation to remove caval thrombi and cavoatrial septic material, respectively. This extracorporeal circuit configuration allowed adequate respiratory support during the procedure. No endovascular recurrence of the pathologic material was found at 2 and 1 year of follow-up, respectively.