The aim of this study was to compare the amount of residual organic debris on endodontic instruments that had been cleaned in either an ultrasonic bath or a washer disinfector prior to sterilisation. A total of 90 endodontic files of varying sizes were used to clean and shape root canals in extracted teeth and were then placed in endodontic file holders. Test group 1 (36 files) were ultrasonically cleaned for 10 min and test group 2 (36 files) were cleaned in a washer disinfector. A control group (18 files) were not cleaned at all. Following sterilisation, all the files were visually inspected under a light microscope and scored using an established scale. The results showed that both test groups had significantly less residual debris than the control group. Comparing the test groups, the files that had been cleaned ultrasonically had significantly less debris than those cleaned in the washer disinfector. The design of the instrument holder may have been a factor in this result. More research is needed into the use of washer disinfectors in the cleaning of small dental instruments that have a complex surface structure.