Most peanut allergens are seed storage proteins, and Ara h 1, Ara h 2 and Ara h 3 are classified as the major peanut allergens. In contrast to Ara h 1 and Ara h 2, Ara h 3 has several homologous proteins such as Ara h 4, Ara h 3/Ara h 4 and gly1 in peanut seed. We isolated a novel ara h 3 cDNA clone, ara h 3-im, and the presence of Ara h 3-im in peanut seeds was confirmed by N-terminal sequence analysis. Ara h 3-im shows 75% sequence homology with other Ara h 3-related proteins and contains only three out of four Ara h 3 epitopes which can be recognized by IgE. However, Ara h 3-im shares structures in common with other plant 11S globulin proteins. The corresponding mRNAs of the ara h 3-related genes accumulate only in developing seed and were localized in the cotyledons of mature seed. On SDS-PAGE, Ara h 3-im was not recognized by the IgE of serum from a peanut allergic patient. Therefore, Ara h 3-im may have lower allergenic properties than other Ara h 3-related proteins.