In Japan, an increasing number of people suffer from pollenosis, a typical atopic disease. Japanese cedar (Cryptomeria japonica) pollen is the most common allergen that causes pollenosis. Although Cry j 1 and Cry j 2 are the common allergenic proteins contained in the pollen, there is a small population of patients who exhibit positive skin reactions to the pollen extract but are negative for both Cry j 1 and Cry j 2. This suggests that the pollen may contain other antigenic proteins besides these two molecules. In this study, we used sodium dodecyl sulfate-polyacrylamide gel electrophoresis to examine partially purified pollen extract (PPPE) and determine if there were other proteins that reacted to anti-PPPE sera collected from sensitized guinea pigs, mice and rabbits. Subsequently, we detected four bands of proteins with molecular weights around 7, 15, 20 and 31 kDa, which were different from those normally seen for Cry j 1 and Cry j 2. Among these, the 7, 15 and 20 kDa proteins could not be detected when anti-Cry j 1 monoclonal anti-body (mAb) and anti-Cry j 2 mAb were used as antibodies for Western blotting. Therefore, these three proteins may differ from Cry j 1 and Cry j 2 not only in molecular weight but also in antigenicity. In conclusion, three new antigenic proteins that are not identical to Cry j 1 and Cry j 2 have been shown to exist in Japanese cedar pollen. Structural analyses of these proteins may be useful in the development of new therapeutic methods, including specific immunotherapy for pollenosis.