Correction of congenital heart disease in newborns under extracorporeal circulation is accompanied by fluid overload. To eliminate this pathological state, the method of ultrafiltration is commonly used. The paper presents a comparative analysis of two methods of ultrafiltration in the arterial switch procedure in 20 newborns with transposition of the great vessels. In group I (n = 10) we conducted conventional ultrafiltration during cardiopulmonary bypass; and in group II (n = 10), modified ultrafiltration after completing the cardiopulmonary bypass was used. The data obtained indicate that the inotropic support, the need in blood transfusion during the immediate follow-up and the mechanical ventilation duration were significantly lower during modified ultrafiltration as compared to conventional one.