Oligodeoxynucleotides containing unmethylated CpG dinucleotides (CpG DNAs) prevent development of T-helper type 2 (Th2) immune responses and reverse established allergic responses in mouse models. We recently reported that second-generation immunomodulatory oligonucleotides (IMOs) containing novel structures (immunomers) and a synthetic immunostimulatory CpR (R=2′-deoxy-7-deazguanosine) motif induce the production of distinct cytokine secretion profiles in vitro and in vivo. In the present study, we evaluated IMOs containing CpG and CpR motifs to modulate allergen-induced Th2 immune responses in prevention and treatment models. Mice sensitized and challenged with ovalbumin (OVA) were treated with a CpG DNA or an IMO by administration either at the time of OVA sensitization (co-administration; prevention) or after establishment of an allergic response (treatment). Spleens, blood, and lungs were collected and analyzed for immune responses. Spleen-cell cultures harvested from OVA-sensitized mice showed a significant decrease in Th2 cytokine levels with a concomitant increase in Th1 cytokine levels only when CpG DNA or IMOs were co-administered with OVA. The co-administration of CpG DNA or IMOs during OVA sensitization significantly reduced serum OVA-specific and total IgE levels in mice. The mice who received CpG DNA or IMOs co-administered with OVA showed a small reduction in serum OVA-specific and total IgG1 levels and a significant increase in serum OVA-specific and total IgG2a levels. Similar results were found in mice with established allergic responses who received IMO treatment. IMO treatment also resulted in strong inhibition of inflammatory cell infiltration and goblet cell hyperplasia in the lungs compared with untreated mice lungs. These data demonstrate that IMOs prevent antigen-induced Th2 immune responses when co-administered to mice during OVA sensitization and that IMOs reverse established allergic responses induced by OVA.