In this study, we characterized the physical form of allergenic Cry j 1 in the urban atmosphere. Through an immunofluorescence antibody method, we showed that allergenic Cry j 1 exists as fine particles (≤1.1 μm). To determine Cry j 1 concentrations and its particle size distribution, we used the ELISA method to confirm that most Cry j 1 exists as fine particles in the urban atmosphere and is found at high concentrations on fine day next to rainy day. Furthermore, we evaluated Cry j 1 denaturation by using the Biacore J system based on the surface plasmon resonence (SPR) principle and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). We showed that the dissociation constant (KD) of Cry j 1 that has been exposed to urban polluted air is lower (1.76 ×10-14 M) than that of Cry j 1 (1.32×10-9-3.37×10-9 M) of original pollen grains that has not been exposed to air pollutants. Cry j 1 turns into low molecular weight proteins by reacting with various acidic solutions. In sum, we showed that allergenic Cry j 1 exists as fine particles that can deposit in the lower respiratory tract. This finding clarifies the relationship between Japanese cedar pollinosis and air pollutants.