Bacterial DNA or synthetic oligodeoxynucleotides (ODN) containing unmethylated CpG dinucleotides within the context of certain flanking bases (CpG motifs) have potent stimulatory effects on the vertebrate immune system. CpG ODN with a synthetic nuclease-resistant phosphorothioate backbone (S-ODN) can be used as an adjuvant to augment both humoral and cell-mediated immune responses against a protein antigen. It has also been shown that the presence of CpG motifs in DNA vaccines may be responsible, at least in part, for their efficacy. Here we evaluate the possibility of using CpG ODN as an adjuvant with DNA vaccines to further improve their efficacy. We show that it is not possible to directly mix S-ODN with plasmid DNA because this will result in an ODN dose-dependent reduction in gene expression from the plasmid, possibly because of competitive interference at binding sites on the surface of target cells. Although ODN with a phosphorothioate-phosphodiester chimeric backbone (SDS-ODN) do not adversely effect the level of gene expression (except when certain sequences, such as a poly G, are present), this is not useful, as SDS-ODN are apparently also not sufficiently nuclease resistant to exert a strong CpG adjuvant effect. Neither is it possible to augment responses to DNA vaccines by administering the CpG S-ODN at a different time or site than the plasmid DNA. Thus, at least for the present, it appears necessary to clone CpG motifs into DNA vaccine vectors to take advantage of their adjuvant effect.