BACKGROUND AND AIM: This study was carried out to compare three different ultrasonic cleaner devices in the cleaning process of endodontic instruments by scanning electron microscope (SEM). METHODS: In this study, 120 unused brand new hand and rotary instruments were examined after removing from the sealed package. The instruments were randomly divided into six groups of 20 rotary or hand files each and observed by SEM before ultra-sonication. Then, every pair of hand and rotary instruments was cleaned using one of the ultrasonic cleaner brands. Again the instruments were examined by SEM and assessed in three different parts, tip, middle and distance 16 (D16). SEM data were analyzed by Kurskal–Wallis and Mann–Whitney tests. RESULTS: The tip of the endodontic instruments was the most contaminated area before ultrasonic cleaning. Statistical analysis showed that all of the tested ultrasonic devices were significantly effective machines for debris removal from endodontic instruments. The hand and rotary instruments cleaned by one of the devices were significantly cleaner than the others (P < 0.050). There was a significant difference in cleaning of the separate parts of the instruments during ultra-sonication among ultrasonic cleaners. The tips of the instruments were significantly cleaner than the D16 parts (P < 0.050). CONCLUSION: Various ultrasonic devices have different ability for cleaning of endodontic instruments.