Recently three different neonatal extracorporeal membrane oxygenation (ECMO) circuits have been employed in our clinic. These circuits were compared for clotting and bleeding complications. Initially, we used an ECMO circuit containing a roller pump and venous bladder without severe complications. Manufacturing of circuit components was discontinued, necessitating the replacement of this circuit by a circuit with a centrifugal pump with 3/8 inch inlet and outlet. Acute increase of oxygenator resistance requiring emergency changeout became unexpectedly a regularly occurring complication. The increase in resistance was suspected to be caused by oxygenator clotting, although oxygenator function was preserved. To prevent this complication, we changed to a levitating centrifugal pump with 1/4 inch inlet and outlet, after which no oxygenator malfunction has been observed. Macroscopic and electron microscopic analysis demonstrates that small clots are formed within the circuit, presumably in or near the centrifugal pump, which are transported to the oxygenator and clog up the hollow fiber layer at the inlet side, barely penetrating the oxygenator beyond this first layer. Our results suggest that low blood velocities accompanied with recirculation of blood within or near the centrifugal pump and/or heat generation within the pump could contribute to the formation of these clots.