The worldwide increase in the incidence of allergic diseases and the limited efficacy of current vaccines require the development of new efficient vaccination strategies. Based on PTD (protein transduction domain) technology, we have engineered MAT (modular antigen translocation) molecules, aimed to enhance antigen presentation through intracellular targeting of the MHC II presentation pathway. MAT vaccines consist of a cloning cassette, which fuses Tat (transactivator of transcription) peptide to a truncated Ii (invariant chain), which is able to target antigens to the nascent MHC II molecules in the trans-Golgi compartment. To test the efficacy of intracellular targeting, we engineered arrays of MAT-fusions and compared the effects of recombinant allergens, Tat-conjugated allergens and MAT-conjugated allergens for the ability to stimulate T-cell proliferation and cytokine production in human PBMC (peripheral blood mononuclear cell) cultures derived from allergic individuals, and to elicit protective immune responses in mice. MAT-vaccines induced a strong proliferation of PBMCs at a low concentration and induced a Th2/Treg (regulatory T-cell) cell shift in the cytokine profile, reflecting those reported in successfully desensitized allergic individuals. In allergic mouse models, we showed that MAT-vaccines are highly efficient in desensitizing mice and protect them from anaphylactic shock. The technology is applicable not only for the treatment of allergies, but also for the development of preventive vaccines in general.