Recent advances in molecular biology, genomics, and immunology are revolutionizing our approach to managing infectious diseases of humans, livestock, and poultry. One of the most interesting additions to the armamentarium of research focusing on controlling infectious diseases has been a better understanding of how the host's innate immune system recognizes "danger" signals. Additionally, there has been recognition of the relationship between the innate and the specific arms of the immune system. For example, the recent discovery that CpG motifs can modulate immune responses has been used both as an adjuvant to enhance the responses to vaccines, as well as a direct immunostimulant to prevent infections. Using an Escherichia coli chicken model, we have been able to prevent cellulitis in chickens with CpG alone. Thus, CpG can be used immunoprophylactically to reduce infectious diseases. In addition, we will describe how CpG formulations with various antigens; recombinant proteins, peptides, and conventional vaccines can enhance immune responses to each of these different vaccine combinations. What is even more interesting is that CpG incorporation in vaccines can shift the immune response from a predominant T helper 2 (Th2)-like immune response generally induced by killed or subunit proteins to a much more balanced Th1-Th2 response. These immunomodulatory effects have significant implications for management of infectious diseases of all vertebrates.