OBJECTIVE To screen and identify differentially expressed proteins between adult female and male worms of Schistosoma japonicum(S.japonicum). METHODS Two rabbits infected with the cercaria were perfused with saline in carotid, and approximately two hundred adult female and two hundred male worms of S.japonicum were collected. Approximately 300 microg soluble and hydrophobic proteins of adult female and male worms of S.japonicum were extracted and then the proteins were separated by two-dimensional gel electrophoresis respectively. The analysis using ImageMaster Platinum 2D 5.0 resulted in differentially expressed proteins between adult female and male worms, which were subjected to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and tandem mass spectrometry sequencing of tryptic peptides. RESULTS There were (255 +/- 10) and (224 +/- 12) spots detected for soluble proteins and (200 +/- 11) and (132 +/- 8) spots for hydrophobic proteins from adult female and male worms respectively. Six differential proteins were identified, five up-regulated proteins in female worms were thioredoxin, putative ferritin-1 heavy chain, chain B in solution structure of the human ubiquitin-conjugating-enzyme-like protein Mms2-Ubiquitin Complex, heat shock protein 10, cytoplasmic fatty acid binding protein variant H; while only one up-regulated proteins in male worms was identified as 48 kDa histamine receptor subunit peptide 4. CONCLUSIONS Several differentially expressed proteins between female and male worms of S. japonicum were recognized through screening and identifying differential proteins between female and male worms of S.japonicum.