Pollen of genetically modified (GM) pepper containing the gene for cucumber mosaic virus (CMV) coat protein (CP) and GM Chinese cabbage with high phenylethylisothiocyanate (PEITC) content was investigated for assessment of allergic risk. Amino acid (AA) sequences of the inserted gene products of GM virus resistant pepper and GM Chinese cabbage with high PEITC content were compared with those of known allergens. No known allergen greater than 35% AA sequence homology, over 80 AA window or more than 8 consecutive identical AA was found. Protein patterns of GM/non-GM pepper and Chinese cabbage pollen extracts in SDS-PAGE analysis showed the same distribution of protein bands among the GM and non-GM pepper or Chinese cabbage, respectively. Sera from pollen allergic patients showed some IgE reactivity via immunoblotting and ELISA; however, no differences were observed between the pollen of GM and non-GM pepper or Chinese cabbage, respectively. Based on these results, we conclude that pollens of the virus resistant GM pepper and GM Chinese cabbage with high PEITC have no differences in their protein composition or allergenicity relative to non-GM pepper and Chinese cabbage.