Objective Efforts were made to investigate the effects of continuous venous-venous hemofiltration (CVVH) on the markers for endothelial injury in systemic inflammatory response syndrome and sepsis (SIRS/sepsis) patients. Methods Soluble thrombomodulin (sTM), soluble intercellular adhesion molecule-1 (sICAM-1), soluble E-selectin in plasma were measured by ELISA before and after CVVH treatment in 15 SIRS/sepsis patients. APACH II scores were used to evaluate the CVVH effects. Results APACH II scores improved on the 4th day after the treatment in 8 SIRS patients, but worsened in 7 sepsis patients. Plasma sTM, sICAM-1 and E-selectin were significantly higher in SIRS/sepsis patients than in normal controls, and were higher in sepsis patients than in SIRS patients. On the 7th after the treatment, plasma sTM and sE-selectin decreased remarkably in SIRS patients but not in sepsis patients. Conclusion Endothelial activation and injury occur in SIRS/sepsis patients. CVVH can partially improve the endothelial function in SIRS patients but not in sepsis patients.