Recognition of danger of infection by innate immune cells is a prerequisite to combat infections and to activate T and B cells. Pathogen-associated molecular patterns (PAMP) play a fundamental role in this process. PAMPs are sensed by at least ten different Toll-like receptors (TLR). Within the realm of PAMPs, CpG DNA that is recognized by TLR-9 has an outstanding propensity to induce a milieu that favors activation of T lymphocytes and biases Th1-dominated immune responses. Therefore CpG DNA has become a promising immuno-therapeutical candidate to assist and to direct immune responses such as in vaccination or modulation of allergic responses. As opposed to other PAMPs, CpG DNA can be synthesized with defined purity and base composition. Moreover, chemical substitutions can confer new qualities to synthetic CpG DNA.