The objective of this study was to evaluate the effect of flow rate, negative pressure, and duration on modified ultrafiltration (MUF). Eighty children weighing less than 10 kg with congenital heart disease were randomly divided into four groups: group C (conventional MUF); group H (high flow rate MUF); group P (high negative pressure MUF); and group L (long duration, high flow rate MUF). The changes in body weight, hematocrit, and hemodynamics were recorded. Tumor necrosis factor and interleukin-6 were measured before bypass, bypass stop, and MUF cessation. The durations of MUF in groups H and P were significantly shorter than in the other two groups; the volume filtered in group L was much greater than in the other three groups. The changes of bodyweight, heart rate, blood pressure, and hematocrit were similar in all groups. The increased extent of inflammatory mediators was a little lower in group L. Modified ultrafiltration can reverse hemodilution and improve cardiac function even with high flow rate or negative pressure. Prolonging the duration of MUF can filter out more inflammatory mediators, but the increased trend cannot be reversed in 15 minutes.