In order to understand the mechanism of growth and development of Schistosoma japonicum, the differentially expressed gene cDNA libraries of Schistosoma japonicum cercariae, egg and adult worm were constructed separately for the first time by SSH (suppressed subtractive hybridization) technique, which can be used to isolate and analyze differentially expressed genes on the whole genome scale. The results of subtractive efficiency and identification of stage difference among above three subtracted cDNA libraries indicated the quality were high. The 257 clones which inserted fragments more than 500 bp from above three cDNA libraries were sequenced. BLASTn results showed that these 257 ESTs represented 182 schistosome genes, including 22 schistosome known genes, 128 schistosome ESTs and 32 no match genes which may represent schistosome novel gene. Results of these ESTs function prediction indicated that differentially expressed genes from cercariae subtracted cDNA library were mainly involved in movement, energy metabolism, transcriptional regulation and pathogenesis; differentially expressed genes from egg were mainly involved in signal transduction, cell adhesion, protein and carbohydrate metabolism and response to oxidative stress; differentially expressed genes from adult worm were mainly involved in protein biosynthesis, transport and body movement. To isolate and analyze differentially expressed gene on large scale must provide the valuable information for understanding the mechanism of parasite growth and development on the molecular level, for screening highly effective antigen candidates, target of drug and diagnostic antigen.