AIM: To compare using scanning electron microscopy (SEM) root canal walls following instrumentation in vitro with two different rotary NiTi instruments. The hypothesis was that no difference should be observable between the experimental groups in terms of debris on canal walls and surface morphology. METHODOLOGY: Twenty-four single-rooted human teeth were selected. Two types of NiTi instruments were used, Mtwo (Sweden & Martina, Padova, Italy) and ProTaper (Dentsply Maillefer, Ballaigues, Switzerland). Irrigation for both groups was performed after each instrument change with 5% NaOCl, 3% H2O2 and 17% EDTA solutions. Three different areas (coronal, middle and apical thirds) of the root canal were evaluated using SEM. The canal wall of each sample was assessed and compared using a predefined scale of four parameters, namely, smear layer, pulpal debris, inorganic dentine debris, surface profile. Data were analysed statistically using the Kruskal-Wallis test (anova). RESULTS: A statistically significant difference (P