Recent advances in immunology reveal that vertebrate innate immune systems use pattern-recognition receptors, of which the best characterized is the toll-like receptor (TLR) family, to specifically detect pathogen-associated molecular patterns (PAMPs) present in infectious agents. Based on this, use of synthetic PAMPs has attracted much interest for specific immunoprophylaxis and immunotherapy purposes. Among the PAMPs, immunostimulatory CpG DNA, a TLR9 ligand, displays promising potent immunostimulatory and adjuvanticity in different settings. In this review, recent developments in the use of CpG DNA for inducing immunity in the mucosal tissues will be highlighted.