E. histolytica proteins that were present in 1 or more cyst preparations and those that were not found in trophozoite proteome or trophozoite EST datasets were categorized in various functional categories based on their annotations in the database. Out of a total 195 proteins, 77 did not have any known function, and they are designated as hypothetical proteins. Four E. histolytica cyst-wall specific proteins (such as Jacob, 2 chitinases and chitin synthetase) were present in 1 or more cyst preparations. A total of 60 various enzymes (including 19 protein kinases, 10 GTPases, 2 chitinase and a chitin synthetase) were also detected. Among other proteins, 8 vesicle coating or trafficking protein, 4 DNA repair proteins, 5 transcription or translation related proteins, 4 surface associated proteins, are notable.