Background: Peanut allergen Ara h 3 has been the subject of investigation for the last few years. The reported data strongly depend on recombinant Ara h 3, since a purification protocol for Ara h 3 from peanuts was not available. Methods: Peanut allergen Ara h 3 (glycinin), was purified and its posttranslational processing was investigated. Its allergenic properties were determined by studying IgE binding characteristics of the purified protein. Results: Ara h 3 consists of a series of polypeptides ranging from approximately 14 to 45 kDa that can be classified as acidic and basic subunits, similar to the subunit organization of soy glycinin. N-terminal sequences of the individual polypeptides were determined, and using the cDNA deduced amino-acid sequence, the organization into subunits was explained by revealing posttranslational processing of the different polypeptides. IgE-binding properties of Ara h 3 were investigated using direct elisa and Western blotting with sera from peanut-allergic individuals. The basic subunits, and to a lesser extent the acidic subunits, bind IgE and may act as allergenic peptides. Conclusions: We conclude that peanut-derived Ara h 3, in contrast to earlier reported recombinant Ara h 3, resembles, to a large extent, the molecular organization typical for proteins from the glycinin family. Furthermore, posttranslational processing of Ara h 3 affects the IgE-binding properties and is therefore an essential subject of study for research on the allergenicity of Ara h 3.