A bacteriological assessment of flexible bronchoscopes that were stored after a reprocessing procedure was performed to determine whether reprocessing removes microbiological contamination and whether the instruments could be used safely after extended storage without repeating the disinfection before bronchoscopy. The microbiological quality of manual and automated reprocessed bronchoscopes was examined by collecting a pre-reprocessing and a post-reprocessing liquid sample from the stored instruments' channels. A qualitative microbiological analysis was performed to evaluate bacterial contamination. Among the 264 pre-reprocessing bronchoscopes, 10 were contaminated (13 human flora strains and 1 environmental strain were detected). After reprocessing, 8 were decontaminated and 2 remained contaminated. Furthermore, 12 other bronchoscopes had a new contamination post-reprocessing (11 human flora and 3 environmental strains were detected). In addition, 2 sampled bronchoscopes were contaminated both pre- and posttreatment. Our findings support the suggestion that reprocessing after storage can be avoided in the safe usage of the instrument if earlier decontaminations are performed correctly. Having found that reprocessing could contaminate bronchoscopes, additional studies are needed to identify the risk factors for contamination and avoid controversial suggestions for first-use reprocessing.