Reperfusion-injury is of enormous impact in vascular and transplantation surgery. Post-ischemic reperfusion failure is one of the main reasons for liver dysfunction after liver transplantation, leads to a very high number of re-operations and increases the demand of grafts. Herein, we investigated, whether CpG-oligodeoxynucleotides (CpG-ODN) that are of high actual interest as immunomodulatory agents would be able to reduce post-ischemic liver tissue injury in rats. Female Sprague Dawley rats were pre-treated with a single intraperitoneal injection of CpG-ODN or a biologically inert control DNA-sequence (each 10 nmol). Three days later, intravital fluorescence microscopy was performed after 90′ of ischemia and 90′ of reperfusion. Tissue damage was quantified by intrahepatic leukocyte adhesion, sinusoidal perfusion failure and hepatocellular apoptosis. Bile production was analysed during the entire experiment as a parameter of hepatocellular excretory function. Whereas bile production was not found improved in CpG-ODN-pretreated animals, intrahepatic leukocyte retention (sinusoidal leukocyte stasis and postsinusoidal leukocyte adherence) was significantly lower in CpG-pretreated animals when compared to control animals. Moreover, post-ischemic reperfusion failure and hepatocellular apoptosis were found significantly reduced. Our study shows tissue-protective effects of immunomodulatory CpG-ODN in liver ischemia-reperfusion and underlines the significance of activation of the immune system on the pathogenesis of reperfusion injury.