Direct observations have shown that the bacteria and fungi that cause device-related and other chronic infections grow in well developed biofilms on the surfaces of biomaterials and of compromised tissues. This mode-of-growth confers on the microorganisms an inherent resistance to host defenses, and antibiotic therapy, and makes these infections very difficult to detect because biofilm bacteria do not produce colonies when plated on the agar media used in routine cultures. We have initiated two comprehensive studies of total joint prostheses, and of non-unions secondary to trauma, in which we use DNA-based (Ibis and 454) methods for the detection of bacteria and an iterative process in which we locate and visualize biofilms using FISH probes and confocal microscopy. The DNA-based detection system confirms culture results, but detects more organisms and determines their sensitivity to antibiotics, and appears to be useful in the management of both types of infection. The use of confocal microscopy and FISH probes to visualize and map biofilms, in relation to orthopedic hardware and affected tissues, confirms the Ibis data and provides useful insights into the etiology of orthopedic infections.