Mycoplasmas are the smallest self-replicating life forms and are attracting considerable interest as model organisms for systems studies. Omics technologies have revealed a variety of transcriptional control mechanisms involving various RNA species, extensive protein-protein interaction pathways and complex post translational protein modification mechanisms. Size and phase variation of dominant surface antigens have also been documented in a number of species. Mycoplasma hyopneumoniae is a primary pathogen in the porcine respiratory disease complex, an economically important disease of swine. We have shown that the archetype adhesin protein P97, operon partner P102 and their paralogs are highly expressed, multifunctional proteins that are displayed on the surface as endoproteolytic cleavage fragments. The process of endoproteolysis is complex with events that are executed with varying efficiency and generate fragments displaying different motif patterns. To date, three cleavage motifs have been characterised but the proteases responsible have not been identified. We have begun to intensively map the surface proteome of M. hyopneumoniae using trypsin shaving and protein biotinylation methodologies. LC-MS/MS analysis of biotinylated surface proteins captured using avidin chromatography led to the identification of an unprecedented number of endoproteolytic cleavage fragments belonging to these adhesin families. The archetype cilium adhesin P97 is extensively processed. Biochemical studies show that P97 is a multifunctional adhesin and that the C-terminus encodes cilia, extracellular matrix and host circulatory molecule binding domains. Binding studies with chemically synthesized overlapping peptides spanning the C-terminus of P97 allowed us to delineate the identity of residues critical for binding fibronectin and plasminogen. To our knowledge, M. hyopneumoniae is unique in the microbial world in that it generates surface protein diversity through controlled endoproteolysis of highly expressed, large mass adhesin families generating a complex array multifunctional fragments that are retained on the cell surface.