Purpose: To investigate the influence and possible pathophysiological mechanism of pulsatile cardiopulmonary bypass (CPR) in various frequencies in pediatric patients undergoing congenital cardiac surgery. Patients and methods: Clinical data and hemodynamic parameters were collected in 80 patients who underwent congenital cardiac surgeries and were perfused in different settings: pulsatile perfusion (PP) in frequencies of 30 beats/min, PP 60 beats/min, PP 100 beats/min and non-pulsatile perfusion (NP). Serum proteins, plasma-free hemoglobin (PFH), endothelin-1 (ET-1) and nitric oxide (NO) were collected to study possible pathophysiological changes, possible hematological injury and oxidative status under different perfusing conditions. Results: Patients in all groups had similar baseline characteristics, aortic cross-clamping time and CPB duration. More effective pulse gradient (PG), energy-equivalent pressure (EEP) and surplus hemodynamic energy (SHE) were observed in pulsatility with lower frequency setting, under which more patients achieved physiologically normal mean arterial pressure (MAP), without the support of inotropic agents during bypass. Significant between-group differences of serum proteins and PFH were absent the whole time during and after bypass, while a relatively lower percentage of perioperative requirement of diuretics was observed in the low frequency pulsatile group. A better performance to oxidative stress was seen in the low frequency group with higher levels of NO and lower concentration of ET-1, and both intergroup differences were found (P<0.01). Satisfactory clinical outcome was obtained on post procedure course in all groups. Conclusion: Pulsatile perthsion with low frequency setting in pediatric patients undergoing congenital cardiac surgery showed better hemodynamic profiles, potential protective effects on vital organs, better oxidative status and satisfactory clinical outcome.