Standard methods are needed to reliably and efficiently assess bacterial contamination of processed medical devices. This article demonstrates a standard operating procedure (SOP) for fluorescence microscopy–based detection of residual bacteria on medical devices (BAC-VIS). BAC-VIS uses a 4',6-diamidino-2-phenylindole (DAPI) stain with fluorescent microscopy to quickly and cost-effectively detect bacterial contamination of processed medical device parts. The BAC-VIS protocol was optimized and achieved greater than 80% staining efficiency and a signal-to-noise ratio of more than 20 using four representative organisms. The SOP was first validated for use on a buildup biofilm model, accessory channels of contaminated clinically used devices, and inoculated endoscope end caps and O-rings. The buildup biofilm model was used to evaluate BAC-VIS after repeated treatment of adherent bacteria with three common high-level disinfectants: glutaraldehyde, ortho-phthalaldehyde, and peracetic acid. Next, BAC-VIS was used to assess clinically used endoscope parts that cultured positive for Gram-negative bacteria. DAPI-stained cells were found on all culture-positive devices, especially in grooves and imperfections on the surface. Finally, BAC-VIS was used to detect bacteria on inoculated endoscope device components. The results showed potential for BAC-VIS to be a valuable tool for industry and academic/medical researchers for investigations of contaminated medical devices. Results obtained using BAC-VIS can increase understanding of the role of design in cleanability, wear, and prevention of contamination and may lead to improvements in materials and design that could make processed endoscope use safer for patients. Of note, this protocol is not for detecting bacteria on scopes or scope parts that will be put back into clinical use.