Recombinant allergens have gained a lot of importance lately for the diagnosis of allergic diseases and for specific immunotherapy. To characterize recombinant allergens and potential hypo-allergenic derivatives thereof circular dichroism (CD) spectroscopy is used widely. It is a convenient, fast method to assess the structural integrity of the recombinant proteins, compare them with the allergens isolated from natural sources, and to determine the effects of mutations on the structural properties. In this paper, we will describe the techniques and the most useful applications of CD spectroscopy to the field of allergy research.