Objective Evaluate the effects of venous-arterial modified ultrafiltration on hemodynamics compared to arterial-venous in children undergoing cardiopulmonary bypass (CPB) for repair of congenital heart defects. Methods Forty patients underwent MUF randomly divided into two groups,group V-A MUF (n =20) and group A-V MUF (n =20) for 10 min after CPB. They were studied before CPB, after CPB, 10 min after CPB, and 30 min after CPB. Haemodynamic data including heart rate, blood pressure, central venous pressure and hematocrit were recorded. Transoesophaegeal echocardiography determined left ventricular posterior wall thickness in end-systole ( LVPWs) and end-diastole (LVPWd) , end diastolic volume (EDV) , end systolic volume (ESV) and ejection fraction (EF) were measured and compared in two groups. Results Patients in V-A MUF maintained better systolic arterial blood pressure at 10 min and 30 min compared with 0 min values after CPB. A significant decrease in EF were observed in both groups immediately after CPB ( P < 0.05 ). Significant increase in EF was observed at 10 min (60% ) and 30 min (46% ) after CPB compared with 0 min value after bypass in V-A MUF (P <0.001 ). In A-V MUF, no such increase in EF was observed. EF were significantly higher at 10 min and 30 min in V-A MUF as compared with A-V MUF (P < 0. 001). There was also significant improvement in posterior wall thickness in V-A MUF (P <0.05). Haematocrit values were not different in duration of postoperative between two groups. Conclusion Veno-arterial modified ultrafiltration is a safe and effective method of improving hemodynamics in children following cardiac surgery.