The prevalence of allergic diseases is rapidly increasing (Bauchau and Durham 2004). Allergen-SIT, which is based on the administration of the disease eliciting allergens or derivatives, is the only treatment which leads to a life-long tolerance towards previously disease-causing allergens due to restoration of normal immunity against allergens. The treatment has been shown to be particularly beneficial in allergic rhinitis, mild and moderate asthma and insect venom hypersensitivity. Whole aqueous extracts of natural allergen source materials such as pollens, mites, moulds and animal epithelia are the basis for therapeutic preparations that are currently used in clinical practice. The extracts are standardized in terms of total allergenic activity, or potency, and possibly the concentration of one individual major allergen, whilst product consistency is assessed in terms of protein and allergen profiles determined by various techniques including electrophoresis and immunoblotting. An extract may contain numerous proteins only some of which are allergens. The composition is determined to a large extent by the qualityoftherawmaterialandthemethodofextraction and purification. Raw materials are provided by certified suppliers and produced under controlled conditions, but nevertheless there are differences. In addition many extracts derived from natural materials contain endotoxin (Trivedi et al. 2003). The use of recombinant DNA technology appears to provide a realistic means of achieving improvements aiming at obtaining of more precisely defined preparations. This technology also provides the possibility to create allergen derivatives with reduced IgE-reactivity, that is to say hypoallergenic molecules that have a reduced risk for inducing undesirable allergic reactions during the course of immunotherapy, but which retain their therapeutic activity. Numerous allergens have now been cloned for research purposes, but as yet only a few have been developed to the stage at which they can be used in clinical studies.