Protein expression profiles of 10 isolates of Mycobacterium paratuberculosis, M avium 18 (formerly M paratuberculosis 18), and 1 isolate each of M avium serotype 2, M avium serotype 8, and M bovis BCG were examined. Protein expression profiles of M paratuberculosis and M avium were similar. However, two-dimensional gel analysis of [35S]methionine-labeled cellular proteins resolved 4 proteins, with molecular mass of 28,000, 32,000, 32,000, and 42,000 daltons, which were expressed in greater amounts in M paratuberculosis than in M avium. Two proteins, with molecular mass of 43,000 and 60,000 daltons, were identified, which were expressed in greater amounts in M avium than in M paratuberculosis. Immuno (western)-blot analysis, using antiserum from 2 cows clinically infected with M paratuberculosis as the primary antibodies, suggested that the 42,000-dalton protein may be specific for M paratuberculosis. Comparison of protein expression profiles may be useful as a tool for differentiating isolates of M paratuberculosis. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of [35S]methionine-labeled extracellular proteins revealed variability among the isolates. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of [35S]methionine-labeled cellular proteins divided the M paratuberculosis isolates into 2 groups on the basis of a difference in the amount of expression of a 28,000-dalton protein. This information may be useful in epidemiologic studies.