High hydrostatic pressure (HHP) is an extreme thermal-physical stress affecting multiple cellular activities. Recently, we found that HHP treatment caused various physiological changes in rice. To investigate the molecular mechanisms of plant response to HHP, we constructed forward and reverse subtracted cDNA libraries of rice seeds treated with 75MPa hydrostatic pressure for 12h by suppression subtractive hybridization in combination with mirror orientation selection. Of 97 clones isolated through microarray dot-blot and sequenced, 45 were unique genes. Among these 45 unique cDNAs, 29 clones showed significant sequence similarity to known genes, 12 were homologous to genes with unknown function, and the remaining 4 clones did not match any known sequences. Most of the genes with known function were involved in metabolism, defense response, transcriptional regulation, transportation regulation, and signal transduction. To our knowledge, this is the first gene expression analysis of rice in response to HHP. The expression profiles of the genes identified in this study provide useful information regarding molecular processes, including alteration of metabolism and adaptation response caused by HHP.