Background Currently anti-inflammatory therapy with steroids for allergic rhinitis need long-term repeated administration, although it is effective. Gene therapy is being suggested to substitute it. The aim of this study was to investigate nonviral vector mediated exogenous gene expression in COS-7 cells in vitro and the effect of intranasal mouse interleukin (mIL)-12 transgene expression on allergen induced eosinophil infiltration of nasal mucosa in a murine model of allergic rhinitis. Methods In vitro COS-7 cells were infected with Epstein-Barr virus (EBV)/lipoplex. The expression of IL-12 p70 in cell culture supernatant was examined by enzyme-linked immunosorbent assay (ELISA). In mice with ovalbumin (OVA) induced allergic rhinitis, EBV/lipoplex was administered by nasal drops before OVA challenge once a day from day 1 to day 10. The expression of EL-12 mRNA and protein, the change of eosinophil count in nasal mucosa and serum total IgE were measured 24 hours after the last challenge. Results EBV/lipoplex could effectively transfect COS-7 cells. The expression of IL-12 p70 in cell culture supernatant was significantly more than in blank control. EL-12 via EBV plasmid vector transduction could be overexpressed in vivo. In pGEG mIL-12 treated models, the nasal mucosa revealed a high level of widespread mIL-12 transduction by immunohistochemistry and in situ hybridization. Histological evaluation revealed marked suppression of eosinophil infiltration in nasal mucosa. The eosinophil count in allergic rhinitis group [(26.5 +/- 9.8)/high-power field (HPF)] was significantly increased over control group [(0.40 +/- 0.52)/HPF] (F=56.94, P < 0.01), while the count in IL-12 gene therapy group [(4.60 +/- 2.63)/HPF] was significantly less than that of allergic group (F=56.9, P < 0.01). Serum total IgE between in gene therapy mice [(88.83 +/- 6.71) ng/ml] and allergic rhinitis mice [(103.1 +/- 5.7) ng/ml] showed a significant difference (F=1216, P < 0.05). Conclusions Nonviral EBV plasmid vector, pGEG mIL-12 was able to overexpress exogenous gene both in vitro and in murine nasal mucosa in vivo. IL-12 overexpression via EBV/lipoplex could stem allergen induced eosinophil infiltration in nasal mucosa in murine models of allergic rhinitis, which may suggest a new cytokine immunogenetic therapy for allergic rhinitis.