It has been shown that preconditioning with lipopolysaccharide reduces infarct size via Toll like receptor 4 signalling. However, it is not known, whether CpG oligonucleotides (CpG ODN) as Toll like receptor 9 ligands are also able to protect the heart against ischemia/reperfusion (I/R) injury. Therefore the interference between CpG ODN and myocardial infarction was studied. Methods: C57Bl/6 mice were exposed to 1 h occlusion and 24 h reperfusion of the LAD. Experimental groups were treated with different CpG ODNs: 1668 (stimulating), H154 and 1612 thioate (5 nmol/animal) or PBS 16 h ahead of occlusion. mRNAs of various cytokines were monitored by RNAse protection assay 2 h after CpG treatment. Infarct size and area-at-risk (AAR) were measured by planimetry. Results: In the 1668 CpG ODN treated hearts TNF, IL-1b, IL-6, IL-9, and IL-10 were increased compared to all other groups. AAR of left ventricle was about 50% in all groups. The ratio between infarcted area and AAR was significantly reduced in 1668 CpG ODN treated mice compared to PBS control mice (10.1±2,6% vs. 30.0±2.7%; M ± SEM). Pretreatment with H154 and 1612 CpG ODN did not induce any reduction of the infarct size. Conclusion: Stimulation with 1686 CpG ODN induces an inflammatory reaction prior to the infaction, which may take part in the protection against I/R injury.