The allergen Ara h 3 has been purified recently from peanuts. In contrast to recombinant Ara h 3, a 60 kDa single-chain polypeptide, the allergen isolated from its native source is extensively proteolytically processed. The characteristic proteolytic processing for 11S plant storage proteins of the glycinin family is observed for Ara h 3 yielding an acidic and a basic subunit, bound by a disulfide bridge. In addition to this, proteolytic truncation is observed for the acidic subunit but not for the basic subunit of Ara h 3. A series of Ara h 3 polypeptides ranging from 13-45 kDa was separated by sodium dodecylsulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and each band was digested by trypsin. Peptides related to the bands were identified and a scheme positioning the different polypeptides in the Ara h 3 sequence has been constructed. Peptide analysis showed sequence heterogeneity at two positions indicating the presence of multiple genes encoding variant, but highly homologous Ara h 3 proteins. The pool of Ara h 3 polypeptides from its native source illustrated that allergen from the peanut is much more complex than the recombinant protein used for epitope mapping experiments. From several Ara h 3 truncation products one or more immunoglobulin E (IgE) binding sites had been removed. Characterization of the allergenicity of Ara h 3 should therefore also include IgE-binding studies with peanut-derived Ara h 3, providing the high degree of variation in the Ara h 3 protein structure, as this is what peanut-allergic individuals are confronted with.