Oligodeoxynucleotide (ODN) sequences containing unmethylated cytidine phosphate guanosine (CpG) motifs prevalent in bacterial DNA attenuate allergic lung inflammation in experimental models of asthma but failed to inhibit eosinophilia and improve lung function in patients with asthma. Bacterial respiratory tract infections exacerbate asthma in humans. Increased eosinophil survival is a critical factor leading to persistent eosinophilic airway inflammation. Apoptosis is regarded as a key mechanism in the resolution of eosinophilic inflammation. The aim of this study was to investigate the effects of bacterial DNA and CpG ODNs on human eosinophil apoptosis in vitro and to elucidate the signalling pathway. Eosinophils were isolated from human peripheral blood by CD16- or CD16-, CD19- and CD304-negative selection. Apoptosis was determined by flow cytometric analysis of relative DNA content, Annexin-V staining and/or morphological analysis. Toll-like receptor 9 (TLR9) expression was studied by using western blotting and intracellular flow cytometry. Bacterial DNA and phosphorothioate-modified CpG ODNs, but not vertebrate DNA, were found to delay spontaneous eosinophil apoptosis. The effect of CpG ODNs was dependent on endosomal acidification and reversed by inhibitory ODN, which suggests involvement of TLR9 pathway. Furthermore, we demonstrated TLR9 expression in eosinophils derived from both atopic and healthy donors. Non-CpG ODNs had occasionally parallel but less profound effect on eosinophil apoptosis, which was not dependent on endosomal acidification. The anti-apoptotic effect of CpG ODNs was dependent on phosphatidylinositol 3-kinase (PI3K) and nuclear factor-kappaB (NF-kappaB) but not mitogen-activated protein kinases (MAPKs) as determined by inhibitor studies. Although our results suggest CpG-dependent involvement of TLR9 in the action of phosphorothioate-modified ODNs, we interestingly found that the anti-apoptotic action of native bacterial DNA in eosinophils is not dependent on unmethylated CpG motifs. This suggests that bacterial DNA contains a currently unknown recognition structure lacking from vertebrate DNA. Bacterial DNA-mediated suppression of eosinophil apoptosis is a novel mechanism for exacerbation of eosinophilic lung inflammation associated with bacterial respiratory tract infection.