This study evaluates the effect of balanced ultrafiltration, modified ultrafiltration, and balanced ultrafiltration with modified ultrafiltration on inflammatory mediators in children's open-heart surgery. Eighty children with congenital heart disease were randomly divided into four groups: control group (C group); balanced ultrafiltration group (BUF group); modified ultrafiltration group (MUF group); and balanced ultrafiltration with modified ultrafiltration group (B+M group). Clinical data of these groups were similar. Tumor necrosis factor (TNF), interleukin-8(IL-8), and E-selectin were measured at the beginning of cardiopulmonary bypass (CPB), 30 min later, at the cessation of CPB, at the cessation of MUF (MUF group and B+M group), and 2 hours postoperatively. During CPB, the concentrations of TNF, IL-8, and E-selectin increased significantly in C and MUF groups and did not change significantly in BUF and B+M groups. In the period of MUF, TNF and IL-8 increased; whereas, E-selectin did not change. The study shows that ultrafiltration can filter out the inflammatory mediators, but only BUF can decrease the concentrations of them. Moreover, MUF only can concentrate blood. Combining both techniques has both effects, but the effect of BUF was offset by MUF.