Allergic diseases, such as allergic asthma, allergic rhinitis, atopic dermatitis, conjunctivitis, urticaria, food allergy, and/or anaphylaxis, are associated with the skewing of immune responses towards a T helper 2 (TH2) phenotype, resulting in eosinophilic inflammation. TH2 cytokines, such as interleukin (IL)-4, IL-5 and IL-13, promote IgE production, mast cell differentiation, and eosinophil growth, migration and activation which then lead to the pathologic abnormalities in allergic diseases. Moreover, the impaired function of regulatory T cells has been noted in allergic diseases. To date, treatments for allergic diseases, such as antihistamines, corticosteroids, bronchodilators and some allergen-specific immunotherapy, are effective but costly and require long-term and recurrent drug administration. Gene therapy has been shown to be an easy, effective, and convenient treatment by delivering the allergen or the therapeutic protein in the form of plasmid DNA in vivo to modulate allergic immune responses. We summarize here the recent advances of gene therapy in allergic diseases and discuss the challenges in clinical application.