Allergic diseases are common, disabling and potentially life threatening. The processes that lead to production of excessive allergen-specific IgE production are highly complex and heterogeneous. While current treatment strategies are limited, recent technological advances have provided a better understanding of underlying disease processes and offered new potential therapeutic targets. Optimal treatment strategies permanently modify underlying inflammatory allergic immune responses (immunotherapy) with long term alleviation of symptoms and minimal side -effects. Although these processes are still not completely understood, methods of modifying allergen recognition by the immune system have already been successful. Here, we review recent developments and future directions in allergen immunotherapy and adjunctive therapies. Specifically, we address the molecular mechanisms of allergen immunotherapy and new techniques including allergen modification, allergen gene vaccination, CpG immunostimulation, and peptide immunotherapy. Other non-allergen specific molecular targets (including receptor, cytokine and IgE targets) which may complement specific immunotherapy are also discussed. Ideally these methods will eventually be replaced by strategies targeting the prevention of allergic responses (immunoprophylaxis).