Objective To compare the changes between deep hypothermic circulatory arrest (DHCA) with deep hypothermic low flow (DHLF) cardiopulmonary bypass (CPB) on pulmonary surfactant (PS) activity in infants with congenital heart disease. Methods Twenty infants with ventricular septum defect and pulmonary hypertension were assigned to either DHCA group or DHLF group according to the CPB methods respectively. Measurements of saturated phosphatidylcholine /total phospholipids (SatPC /TPL), saturated phosphatidylcholine/ total protein (SatPC/TP) and static pulmonary compliance were performed before institution of CPB, 5 minutes after cessation of CPB and 2 hours. Results The length of ICU stay in DHLA group was significantly longer ( P lt;0 05) than that in DHCA group. SatPC/TPL, SatPC/TP and static pulmonary compliance in DHLF group were significantly lower compared with DHCA group ( P lt;0.01). Conclusion DHLF could lower the PS activity level significantly as compared with DHCA in infants with congenital heart disease.