Allergen-specific immunotherapy is the only treatment that provides long lasting relief of allergic symptoms. Currently, it is based on repeated administration of allergen extracts. To improve the safety and efficacy of allergen extract-based immunotherapy, application of hypoallergens, i.e. modified allergens with reduced IgE binding capacity but retained T-cell reactivity, has been proposed. It may, however, be difficult to predict how to modify an allergen to create a hypoallergen. Directed molecular evolution by DNA shuffling and screening provides a means by which to evolve proteins having novel or improved functional properties without knowledge of structure-function relationships of the target molecules. With the aim to generate hypoallergens we applied multigene DNA shuffling on three group 2 dust mite allergen genes, two isoforms of Lep d 2 and Gly d 2. DNA shuffling yielded a library of genes from which encoded shuffled allergens were expressed and screened. A positive selection was made for full-length, high-expressing clones, and screening for low binding to IgE from mite allergic patients was performed using an IgE bead-based binding assay. Nine selected shuffled allergens revealed 80-fold reduced to completely abolished IgE binding compared with the parental allergens in IgE binding competition experiments. Two hypoallergen candidates stimulated allergen-specific T-cell proliferation and cytokine production at comparable levels as the wildtype allergens in patient peripheral blood mononuclear cell cultures. The two candidates also induced blocking Lep d 2-specific IgG antibodies in immunized mice. We conclude that directed molecular evolution is a powerful approach to generate hypoallergens for potential use in allergen-specific immunotherapy.The large increase in allergic diseases observed during the past decades has urged the development of safe and efficient treatments of allergy. Many new concepts based on targeting the underlying immunological causes of IgE-mediated allergy have been suggested (1-5). However, the only treatment that causes a long-lasting relief of symptoms is allergen-specific immunotherapy (ASIT).3 Today ASIT is based on the repeated administration of allergen extracts prepared from the allergen source. Although successful clinical outcomes are well documented, several problems are associated with allergen extractbased ASIT, including the risk of inducing local and systemic side effects and induction of new sensitizations (6, 7).Large batches of well defined single allergen components can be produced using recombinant techniques, making it feasible to solve problems linked to allergen extract-based ASIT. The most severe side effects of ASIT are caused by the binding of injected allergen to allergen-specific IgE on high affinity Fc⑀RI receptor-bearing effector cells, leading to cross-linking of the Fc⑀RI receptors, degranulation, and release of anaphylactogenic mediators. Therefore, allergens with reduced IgE binding capacity have been proposed to improve the safety of ASIT (8...