Background: Paediatric cardiovascular surgery with or without cardiopulmonary bypass induces a complex pattern of pro- and anti-inflammatory responses. It is suspected that they may contribute to changes on the vascular endothelium. The endothelial response to cardiosurgical trauma and cardiopulmonary bypass, especially in children, has yet to be well established. Patients and methods: We studied 29 children undergoing cardiovascular surgery with cardiopulmonary bypass, comparing them with 21 not undergoing bypass. The groups did not differ significantly with respect to age, sex, weight and preoperative parameters. Blood samples were drawn 24 h before surgery, after onset of anaesthesia, after onset of cardiopulmonary bypass and after rewarming in those undergoing bypass, or immediately after surgery in the control group, 4 h and 2 days after surgery, at discharge, and months after surgery during out-patient follow-up. Serum levels of soluble E-selectin, P-selectin and P-selectin glycoprotein ligand-1 were measured by enzyme-linked immunoassay. Results: Paediatric cardiovascular surgery leads perioperatively to the significant decreases of the serum levels of soluble P- and E-selectin, as well as of soluble P-selectin glycoprotein ligand-1 (all p < 0.05). The time course, and all concentrations, of these molecules were not significantly different with and without bypass. The decreases, however, were more pronounced with cardiopulmonary bypass. Preoperative baseline values were reached months after surgery. Conclusion: Endothelial activation of release of adhesion molecules is reduced during paediatric cardiovascular surgery. Endothelial activity is more perturbed with cardiopulmonary bypass and for a long time after surgery.