In Korea, different kinds of genetically modified (GM) crops are under development, including GM-rice expressing insecticidal crystal (Cry) proteins of Bacillus thuringiensis (Bt) modified to change a single amino acid. In this study, amino acid (aa) sequences of modified Cry proteins were compared to that of known allergens, and Cry proteins expressed in GM-rice were identified by using Cry protein specific polyclonal antibody. The antigen-antibody reactions were compared between GM and commercial rice to assess the allergic risk of Cry proteins. This analysis showed no known allergen to have more than 35% aa sequence homology with modified Cry proteins in Bt rice over an 80 aa window or to have more than 8 consecutive identical aa. Sera from allergic patients showed some IgE reactivity via immunoblotting and enzyme-linked immunosorbent assay (ELISA), although no differences were seen between GM and commercial rice. Based on these results we conclude that GM rice with modified Cry proteins has no differences in its protein composition or allergenicity relative to commercial rice.