Water absorption is a prerequisite for seed germination. During imbibition, water influx causes the resumption of many physiological and metabolic processes in growing seed. In order to obtain more complete knowledge about the mechanism of seed germination, two-dimensional gel lectrophoresis was applied to investigate the protein profile changes of rice seed during the first 48 h of imbibition. Thirtynine differentially expressed proteins were identified, including 19 down-regulated and 20 up-regulated proteins. Storage proteins and some seed development- and desiccation-associated proteins were down regulated. The changed patterns of these proteins indicated extensive mobilization of seed reserves. By contrast, catabolism-associated proteins were up regulated upon imbibition. Semi-quantitative real time polymerase chain reaction analysis showed that most of the genes encoding the down- or upregulated proteins were also down or up regulated at mRNA level. The expression of these genes was largely consistent at mRNA and protein levels. In providing additional information concerning gene regulation in early plant life, this study will facilitate understanding of the molecular mechanisms of seed germination.