Background: Effects of direct hemoperfusion with a cytokine-adsorbing column, CTR, on endotoxin-induced experimental acute lung injury in rats were evaluated. Methods: 36 Sprague-Dawley rats were ventilated mechanically and allocated to one of the following three groups (n = 12 per group): saline control, saline instilled into trachea; endotoxin control, endotoxin (40 mg/kg) instilled into trachea, and treatment group, CTR treated for 90 min after endotoxin (40 mg/kg) instillation. Blood gases, cytokine concentrations and lung histopathology were evaluated. Results: The decreased Pa O<sub>2</sub> in the treatment group had recovered at 120 min after instillation and was significantly higher than that in the endotoxin control. The increased Pa CO<sub>2</sub> in the endotoxin control was significantly higher than that in the treatment group. The elevated cytokine concentrations and the neutrophil infiltration into the lungs were less in the treatment group than in the endotoxin control. Conclusion: The present study showed that CTR treatment inhibited hypoxia, hypercapnia, and inflammatory responses in an acute lung injury model.