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Indwelling prosthetic joints may become colonized by microbial biofilms, although the biofilm structure, composition of the microbial community, and physiologic activity of the organisms in these devices are not well understood. New approaches that rely on the use of fluorescent stain technology can be used to characterize the structure and community composition in a way that earlier methods, which relied on culturing or scanning electron microscopy, could not. Model systems incorporating parameters relevant for indwelling prosthetic joints also can be designed to evaluate the efficacy of treatments for preventing or eradicating biofilms from these devices. Effectively treating microbial biofilms on indwelling medical devices such as prosthetic joints is a challenging proposition. A clearer understanding of the process in vivo and a defined approach for evaluating treatment strategies provide the best hope for success.