Cry j 1 is one of the major allergens in Japanese cedar pollen. We attempt high throughput analysis and comprehensive identification of the linear IgE epitopes of Cry j 1. A series of overlapping synthetic Cry j 1 peptides chemically spotted on cellulose membrane was probed with sera from patients in Japan and United States, which were reactive to Cry j 1, and the reactivity of one of the detected sequences was confirmed by means of competitive ELISA using peptide as coated antigen. The peptide (331)NGNATPQLTKNA(342) (peptide 166) was detected by all three pooled sera used, and peptide (103)NGGPCVFIKRVS(114) (peptide 52) was detected by two of the three pools of sera. In addition, several peptides reacted with one of the pooled sera. IgE binding to peptide 166-coated wells was inhibited by addition of peptide 166 for several individual patient sera, suggesting that peptide 166 is one of the linear epitopes of Cry j 1. Since patients in United States were suggested to be rarely sensitized with Japanese cedar, they were sensitized with the similar tree pollen allergens such as Cup s 1 and Jun a 1, and cross-reacted with Cry j 1. We have comprehensively investigated human IgE epitopes of Cry j 1 and succeeded in identifying a common linear epitope, (331)NGNATPQLTKNA(342).