The identification of unintended effects resulting from genetic modification processes is an important aspect of evaluations of the biosafety of genetically modified organisms (GMOs), but one that is notoriously difficult. Non-targeted techniques, such as proteomics, offer considerable potential for improving the detection of unintended effects of genetic modification in crop plants, such as rice. 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 at the biochemical level, compared to each line’s non GM counterpart, determined. The results indicated that some of the seed proteins from the two transgenic rice lines differed in their relative intensities compared with in their respective control lines. 28 proteins were successfully identified with MALDI-TOF-MS, 5 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 could raise concerns regarding their potential risks for human health and ecology. 