Through nutritional quality assessment and 2D gel electrophoresis, the substantial equivalence study was performed by comparing transgenic Xa21 rice with the non-transgenic IR72 rice in order to characterize the changes resulting upon insertion of Xa21 gene in the genome of IR72 rice. The nutritional quality assessment, which included comparison of amino acid, mineral, and vitamin content, revealed no statistically significant differences between the Xa21 and IR72 varieties, with all differences lying within the reference ranges provided by the OECD ( Gayen et al., 2013). While the proteomics study did reveal some level of alteration in the protein profile of the Xa21, none of the altered proteins were found to be toxic, allergenic, or detrimental to the growth capabilities of the transgenic rice. Notably, the proteomics analysis revealed that a majority of the differentially expressed, up-regulated proteins of the Xa21 rice are involved in plant defense mechanisms, starch biosynthesis pathways, and nutritional component storage, thus contributing some possible advantages to this transgenic variety over the IR72 rice. The result of this entire study of nutritional components and proteome profile of transgenic Xa21 rice seeds revealed that due to integration of foreign gene, no detrimental changes were observed in the transgenic seeds.