Cardiopulmonary bypass constitutes an injury that may cause postoperative pathophysiological changes due to systemic inflammatory response syndrome (SIRS) and multiple organ dysfunction syndrome (MODS). These complications include coagulopathy, hypotension, capillary leakage, and multiple organ injury. To investigate the role of endotoxin and cytokines in the response to bypass injury, we measured plasma levels of endotoxin and proinflammatory cytokines in 20 pediatric patients before and after bypass. Clinical data, including duration of injury and tests indicative of SIRS/MODS, were collected. Levels of endotoxin, TNF-alpha, IL-6, and IL-8 but not IL-1 beta were significantly increased after bypass. Most of the cytokines have been found to correlate with each other. Endotoxin did not correlate with duration of bypass, cytokines, or SIRS/MODS. In contrast, TNF-alpha and IL-8 correlated with duration of bypass and were associated with SIRS/MODS. Certain clinical complications were associated with specific cytokines. Understanding the role of cytokinemia in SIRS/MODS may lead to better prognostic assessment and therapeutic modalities.