FDG PET/CT has become a valuable tool in the diagnosis of the activity of chronic osteomyelitis. The surgical strategy in the treatment of chronic osteomyelitis is the identification of the bone focus and radical debridement of sequesters. The aim of the current study was the registration and use of the FDG PET/CT imaging datasets on a navigation system to provide diagnostic imaging based feedback during surgical procedures. For the present study, FDG PET/CT scans were acquired from artificial bones and cadaver bones with a local focus of activity. The DICOM data sets were merged using a navigation system. The referenced regions of interest were matched with fluoroscopic pictures to register the PET/CT DICOM datasets to the bone and direct visual control. Navigated targeting led to accurate results when verified with fluoroscopic images by targeting previously inserted reference points in artificial and cadaver bone. FDG PET/CT datasets are suitable for navigation and compatible with conventional planning and navigation software. The combination of diagnostic FDG PET/CT imaging with surgical navigation techniques could be a valuable tool for the accurate treatment of chronic osteomyelitis.