The proteins and antigens of three strains of Mycoplasma fermentans were compared with those of a mycoplasma, designated "Mycoplasma incognitus," recently identified in tissues of AIDS patients. Previous studies have shown that "M. incognitus" is most likely not a new species but rather a strain of M. fermentans. In the present study, one- and two-dimensional electrophoretic analysis demonstrated the expected similarity between these mycoplasmas, but it also demonstrated several distinct protein differences. Nine proteins were identified as strain variable by two-dimensional gel electrophoresis. Also, immunoblot analysis using rabbit antiserum against the type strain of M. fermentans (strain PG 18) documented the occurrence of size heterogeneity in at least one and possibly two other antigens.