The current generation of allergen products for allergy diagnosis and treatment is based on heterogeneous allergen extracts having an extremely complex, variable, and to a far extend even unknown composition. In contrast, a wide array of major and minor allergens derived from plant pollen, food, and animal can be produced as recombinant proteins. For testing blood sera of allergic patients with highly purified recombinant allergens the term component-resolved diagnosis has been coined. In order to decrease the risk of side-effects of specific immunotherapy research projects have been elaborting hypoallergenic variants by recombinant DNA technology. By binding less IgE the proof of principle has been shown applying in vitro methodology and using animal models. Clinical studies are on demand investigating the therapeutic potential of recombinant allergens. For this purpose standardized material is required and bioanalytical tools for proper characterization have to be developed and validated. According to international standards (ICH guideline Q6B) the physicochemical characterization profiles for biological therapeutics have to specify criteria including identity, quantity, homogeneity, folding, and aggregation. As the allergy research group has a solid record in characterizing purified natural and recombinant allergens at the biochemical and biophysical level we will improve the established and develop new bioanalytical tools for allergen standardization.