The diagnosis and immunotherapy currently applied to allergic diseases involve the use of crude extracts of the allergen source without defining the allergy-eliciting molecule(s). Advances in recombinant DNA technology have made identification, cloning, expression and epitope mapping of clinically significant allergens possible. Recombinant allergens that retain the immunological features of natural allergens form the basis of accurate protein-chip-based methods for diagnosing allergic conditions. The ability to produce rationally designed hypoallergenic forms of allergens is leading to the development of novel and safe forms of allergy vaccines with improved efficacy. The initial clinical tests on recombinant-allergen-based vaccine preparations have provided positive results, and ongoing developments in areas such as alternative routes of vaccine delivery will enhance patient compliance.