In implant infections, a quick and reliable identification of the etiological agent is crucial to realizing efficacious therapies. Among molecular methods, automated ribotyping has proven to be an accurate and rapid technique. More recently, MALDI-TOF/MS and PCR-electrospray ionization (ESI)/MS have been applied successfully to microbiological diagnosis. In implant infections, biofilm is still the major problem for bacterial persistence and recalcitrance to antibiotic therapy. Among biofilm-disrupting agents, enzymes promise the greatest therapeutic possibilities. DNase I degrades biofilm extracellular DNA and has been shown to sensitize biofilm to various biocides and anionic detergents, while dispersin B acts on biofilm exopolysaccharide and, combined with antiseptic, gives a broad-spectrum antibiofilm and antimicrobial activity. The novel antimicrobial approach based on photodynamic treatment (PDT) applies, in combination with antibiotics, to the implant or medical devices reachable by optical fibers. Better progress could be gained by the development of infection-resistant biomaterials able to both inhibit bacterial adhesion and promote tissue integration. New knowledge regarding the fibronectin-mediated internalization of Staphylococcus aureus by osteoblasts, and on its role in the pathogenesis of implant-related osteomyelitis, paves the way for the development of vaccines against staphylococcal adhesins, to prevent both adhesion on biomaterials and bacterial invasion of bone cells.