Immunostimulatory DNA sequences (ISS, CpG motifs) potently stimulate Th1 and cytotoxic T lymphocyte (CTL) responses to antigens and have thus generated considerable interest due to their potential use in immunotherapeutics. An array of cytokines are produced in response to ISS exposure, but the relative importance of each of these mediators in the stimulation of innate and adaptive ISS-induced immunity has yet to be fully investigated. To address this issue, we measured immune responses in mice with targeted deletions of the ISS-induced genes encoding IL-12 (IL-12(-/-)), IFN-gamma (IFN-gamma(-/-)), the IFN-gamma receptor (IFN-gammaR(-/-)), and the IFN-alpha/beta receptor (IFN-alpha/betaR(-/-)) after immunization with ISS-containing oligodeoxynucleotides and model antigens. IL-12(-/-) and IFN-alpha/betaR(-/-) mice were compromised in their ability to develop a cross-primed CTL response, whereas IFN-gamma(-/-) and IFN-gammaR(-/-) mice were not. In addition, lymphocytes from immunized IFN-alpha/betaR(-/-) mice had defective IFN-gamma responses to antigen restimulation. Antigen nonspecific ISS-induced B cell proliferation was normal in the four deficient strains; however, innate IL-6 production was reduced in IFN-gamma(-/-) and IFN-gammaR(-/-) splenocytes and eliminated in IFN-alpha/betaR(-/-) cells. While IL-12 production was defective in only the IFN-gamma(-/-) splenocytes, innate natural killer cell IFN-gamma synthesis was virtually absent in the IL-12(-/-) and IFN-alpha/betaR(-/-) mice. Thus, while IFN-alpha/beta, IFN-gamma, and IL-12 each play important and distinct roles in the development of the innate and adaptive immune responses to ISS, IFN-alpha/beta is a particularly crucial and currently under-appreciated factor in this system.