The identification of unintended effects resulting from genetic modification processes is an important but difficult aspect of evaluations of the biosafety of genetically modified organisms (GMOs). Non-targeted techniques offer considerable potential for improving the detection of unintended effects of genetic modification in crop plants. In this study, total seed protein expression patterns of two strains of transgenic rice (Bt rice and PEPC rice) were examined using a comparative proteomics approach with two-dimensional electrophoresis (2-DE), and differences determined comparing to each line’s non GM counterpart. The results indicated that some of the seed proteins from the two transgenic rice lines differed in their relative intensities. Twenty eight proteins were successfully identified with MALDI-TOF-MS, five of which were well-characterized and these were discussed. In summary, transgenic rice were found to differ in their protein contents from their non-GM counterparts, which might raise concerns regarding their potential risks for human health and ecology.