Modified ultrafiltration is used in cardiac surgery with cardiopulmonary bypass in order to diminish systemic inflammatory response syndrome. We aimed to show its utility for removing pro-inflammatory agents in operated pediatric patients with congenital heart disease and its impact at operative care. A clinical case control trial was designed, including patients with simple congenital heart disease operated on with cardiopulmonary bypass in a 1-year period. We randomized them to a problematic group (with modified ultrafiltration, n = 15) and a control group (without it, n = 16), and blood samples to measure interleukins (6 and 10), 3d and 4d complement fraction concentrations were taken at the following times: baseline, before cardiopulmonary bypass, after it, after modified ultrafiltration, and from the ultrafiltration concentrate. Operative clinical end points of success were defined as hemodynamic stability, absence of morbidity, and lack of mortality. We observed a higher significant interleukin six concentration in the problematic group patients at baseline, as well as a higher removal of this pro-inflammatory agent at the ultrafiltration concentrate. Modified ultrafiltration has a positive impact over simple congenital heart disease surgery with cardiopulmonary bypass because of removing interleukin 6. We recommend its routinely use when hemodynamic conditions are favorable.