The proteins of Mycoplasma pulmonis were examined by two-dimensional polyacrylamide gel electrophoresis and immunoblotting. Comparison of profiles from silver-stained two-dimensional polyacrylamide gel electrophoresis of 18 strains of M. pulmonis allowed identification of five proteins that were strain variable. These variable proteins were not dependent on the medium used to grow the organisms and were shown by reaction with serum samples from naturally infected rats and mice to be produced in vivo and not to be medium components. Identification of strain-variable proteins may lead to an explanation of the differences in properties found among M. pulmonis strains.