When the allergen nomenclature system was adopted in 1986, allergens were identified by their behavior on electrophoresis and chromatography and by reactivity to shared antisera. Not only was this unsatisfactory for standardization, but the processes of allergic sensitization and immunotherapy could not be studied in the framework of antigen processing and B- and T-cell epitopes. Recombinant technologies developed in the 1980s for cloning cDNA from low-abundance mRNA permitted the cloning of allergens, beginning with the major house dust mite allergen Der p 1 and hornet allergen Dol m 5. After this, a wave of cloning with IgE immunoscreening resulted in the cloning of Der p 2, Der p 5, Bet v 1, Bet v 2, and Dac g 2 along with Fel d 1 cloned after amino acid sequencing. Recombinant allergens have now been used to define the important allergens for a wide range of allergies and to develop new types of immunotherapy, some of which have shown efficacy in human trials. The clonally pure allergens have been used to solve the tertiary structures of allergens and from this how allergens might activate innate immunity. Proprietary recombinant allergens are now being used in improved diagnostic tests.