Previously, transgenic soybeans were generated and reported to produce tocotrienols (α-, γ- and δ-tocotrienols), compounds not normally found in soybean. Three procedures were evaluated to optimize the extraction method for transgenic soybean seeds and germinating seeds. Significant differences were observed among the extraction methods in seeds and germinating seeds. In seeds, the highest analytical values (tocopherols, 37.11mg100g −1 ; and tocotrienols, 1.54mg100g −1 ) were observed by using rapid Soxhlet extraction. In germinating seeds, the content of transgenic soybean (B20 and C5) total vitamin E (tocopherols, 18.04, 20.73mg100g −1 ; and tocotrienols, 0.82 and 0.84mg100g −1 ) by direct extraction was approximately 16% and 9% greater than the amount obtained by saponification. In addition, 1,1-diphenyl-2-picrylhydrazyl (DPPH) and 2,2′-azino-bis-(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS) tests demonstrated a direct correlation between the radical-scavenging capacity and the total content of natural tocopherols and tocotrienols. Therefore, these results suggest that an optimal extraction method will provide a fast, simple, reproducible procedure for analyzing tocotrienols and tocopherols. Furthermore, this method may be used to determine novel minor functional compounds such as tocotrienols for the evaluation of biological activity.