Seed germination is a complicated physiological process in which many biochemical processes are initiated or resumed [25]. Thus, large amounts of proteins are changed in this process. In the present study, a comparative proteome analysis of the soybean seeds at different stages of imbibitions (0, 48, 72, 96, 120 h) was performed. Overall, the temporal proteome profiles were quite different. The 2-DE maps showed a highly dynamic proteome during germination (0–24 h), radical elongation (24–72 h) and rapid seedling growth (72–120 h). Differences in the number and the abundance of various spots were analyzed. Interestingly, both the number and intensity of the protein spots below 26 kDa were increased, while the spots between 26 kDa and 43 kDa were decreased during the germination and seedling growth.