Introduction: Elimination of the smear layer after root canal instrumentation requires the use of irrigating solutions. This cleaning can be completed with passive ultrasonic or sonic irrigation. The aim of this study was to evaluate the effectiveness of the Endo Activator System in removing the smear layer after rotary root canal instrumentation, with and without a final flush of 17% ethylenediaminetetraacetic acid (EDTA) solution, in coronal, middle, and apical thirds. Methods: Forty single-canal teeth were decoronated and randomly divided into 4 groups (n = 10). The groups were instrumented by using Mtwo System. Endo Activator was used with a final rinse of 1 mL of 17% EDTA or 4% NaOCl for 1 minute. The roots were longitudinally split and were grooved in the coronal, middle, and apical thirds. Scanning electron microscopy digital photomicrographs at 400 x were taken to evaluate the amount of smear layer in each third. Results: The NaOCl/EndoActivator group did not remove any smear layer of the root canal wall (100% in the coronal, middle, and apical thirds). In the groups that used 17% EDTA (with or without EndoActivator), the smear layer was eliminated completely (100%) in the coronal third, but the amount of removal was less in the other two thirds. The comparisons between NaOCl versus NaOCl/EndoActivator groups and EDTA/NaOCl versus EDTA/EndoActivator/NaOCl groups showed no significant differences in root canal thirds. Conclusions: The Endo Activator System did not enhance the removal of smear layer as compared with conventional Max-I-Probe irrigation with NaOCl and EDTA. (J Endod 2010;36:308-311)