The protein profiles of Blastocystis hominis, B. lapemi, and B. ratti were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and species could be differentiated by this means as well as by Western-blot analysis with polyclonal antibodies. No intraspecies difference could be distinguished between the two B. hominis isolates or the three B. ratti isolates. Western-blot analysis showed extensive cross-reactivity of B. lapemi and B. hominis antigens with anti-B. ratti serum. Some of the cross-reactive antigens were glycoproteins as determined on the basis of their sensitivity to periodate treatment.