Background In studying potential immunotherapeutics for sepsis, we used a lipopolysaccharide (LPS)-stimulated whole blood model to test the immunomodulating capacity of cytosine-phospho-guanine oligodeoxynucleotides (CpG ODNs). We hypothesized that CpG ODNs would have considerable counterinflammatory effects on LPS-induced cytokine production. Methods We administered 4 μmol/L of CpG ODNs (2216, D19, 2006, K3, or 1668) or guanine-phospho-cytosine (GpC) ODNs (control D or control K) immediately after LPS (10 ng/mL) stimulation of heparinized human whole blood. Samples were incubated for 1, 3, 6, 12, and 24 hours. Media and LPS were used as negative and positive controls. Cell-free supernatants were obtained and evaluated for interferon gamma (IFN-γ), interleukin (IL)-12(p40), tumor necrosis factor alpha, IL-6, IL-10, IFN-α, IL-8, and IL-1β by ELISA. Results Compared to LPS alone, significantly reduced levels of IFN-γ, IL-12(p40), tumor necrosis factor alpha, and IL-6 were associated with both CpG and GpC ODNs administration to LPS-stimulated whole blood. IL-10 levels were concomitantly increased. However, IFN-α generation was CpG specific as was increased IL-8 levels. Lastly, only 2216 was associated with decreased IL-1β levels. Conclusions CpG ODNs and GpC ODNs in the LPS-stimulated whole blood model demonstrate differential counterinflammatory effects, but only CpG ODNs were associated with proinflammatory cytokine production. With further examination, we may find that these observed immunomodulatory differences could potentially be exploited for therapeutic benefit.