To assist genetic research into Cryptomeria japonica, which is one of the most important forest tree species in Japan, expressed sequence tag (EST) analysis was carried out. The cDNA clones were isolated from a library derived from inner bark tissues. Partial sequences were obtained from 2231 clones, representing 1398 unique transcripts. Putative functions were assigned to 1583 clones, which represented 882 unique transcripts, by a Blast algorithm. Homology analysis suggested that ESTs related to cell wall formation represented about 3% of the clones. Transcripts of plant stress response genes were also abundant in the inner bark library, especially genes involved in wounding and drought responses. This indicates that the stress response systems of this tree species are similar to those of other plants, and that these systems are highly conserved among plant species. The remaining 648 clones, which represented 516 unique transcripts, did not show any significant homology to known sequences in the databases searched: these are expected to represent genes specific to Cryptomeria and, possibly, to related species.