We predicted that biofilm would form on surfaces of endoscope tubing in contact with fluids, and may be difficult to remove by current washing procedures. Its presence may protect micro-organisms from disinfectant action and contribute to failure of decontamination prior to re-use. Tubing samples removed from 13 endoscopes that had been sent to an endoscope-servicing centre were examined for the presence of biofilm and bacteria by scanning electron microscopy. Biological deposits were present on all samples tested. Biofilm (bacteria plus exopolysaccharides matrix) was present on the suction/biopsy channels of five of 13 instruments, and was very extensive on one of these. Bacteria and microcolonies were often but not necessarily associated with surface defects on the tubing. All 12 air/water channels examined showed biofilm, and this was extensive on nine samples. Routine cleaning procedures do not remove biofilm reliably from endoscope channels, and this may explain the unexpected failure of decontamination encountered in practice despite good adherence to infection control guidelines.