Glutaraldehyde is used to disinfect flexible and other heat-sensitive endoscopes often with the aid of automated systems. Mycobacterium chelonae is being isolated with increasing frequency from these washer disinfectors and processed endoscopes. This has, on occasions, led to misdiagnosis and iatrogenic infections. Recent reports suggest that disinfecting machines, on a sessional or regular basis, with 2% glutaraldehyde may have selected and therefore encouraged the growth of strains of Myco. chelonae, possibly in biofilm, with decreasing susceptibility to glutaraldehyde. In view of this, the resistance of three strains of Myco. chelonae var. chelonae (the type strain NCTC 946 and two machine isolates) was tested against 2% glutaraldehyde and a wide range of alternative disinfectants. Disinfectants tested were a chlorine releasing agent, sodium dichloroisocyanurate at 1000 ppm and 10,000 ppm av Cl, 0.35% peracetic acid (NuCidex, Johnson & Johnson), 70% industrial methylated spirit (IMS), 1% peroxygen compound ('Virkon', Antec International) and 10% succine dialdehyde ('Gigasept', Sanofi Winthrop). Suspension and carrier tests were carried out in the presence and absence of an organic load. Results showed the type strain, which had not been exposed to the selective pressure of disinfectant usage, to be very sensitive to most disinfectants with the exception of 1% Virkon. The washer disinfector isolates, on the other hand, were extremely resistant to 2% glutaraldehyde and showed greater resistance to 1% Virkon and 1000 ppm NaDCC. Purchasing machines in which the entire fluid pathways, including those for delivering rinse water, are disinfected with an appropriate agent during each cycle are preferred. If this is not possible then sessional cleaning and disinfection at the start of each day and regular maintenance should prevent biofilm formation and contamination with disinfectant-resistant strains of mycobacteria. In addition to machine disinfection, the use of sterile or bacteria-free (filtered < 0.45 microm) water is essential for bronchoscopes and all invasive endoscopes. If there is doubt that the effectiveness of the machine disinfection procedure or water quality, the channels and surfaces of endoscopes may be rinsed with 70% IMS after automated processing.