Complete removal of smear layer and debris during the process of root canal therapy is of paramount importance in order to achieve the objectives of endodontic treatment. The aim of this study was to compare the amount of extruded debris and smear layer using two widespread rotary nickel-titanium instruments. Fifty eight freshly extracted human mandibular first molar mesial canals were randomly assigned into two groups. The root canals were instrumented using Mtwo (VDW, Munich, Germany), and BioRaCe (FKG Dentaire, LaChauxde-Fonds, Switzerland) NiTi instruments. Debris and smear layer from the apical thirds part during instrumentation were evaluated by scanning electron microscope. Then, the scores of remaining debris and smear layer were calculated for each group and compared. Data were then statistically analyzed using Mann-Whitney U test. There were significant differences in the amount of smear layer among two groups (P < 0.05). The greatest amount of apical debris was extruded by the BioRaCe group and the least by the Mtwo group. The results of the present study showed that, although both instrumentation techniques apically extruded debris and smear layer through the apical foramen, the Mtwo instruments induced less extruded debris and smear layer than the BioRaCe rotary systems.