This study was to investigate the mode of fracture of ProTaper rotary instruments after clinical use and to compare stereomicroscopy with scanning electron microscopy (SEM) to determine which is the better method for establishing the mode of material failure. In all, 100 fractured ProTaper instruments were examined under stereomicroscope for the presence of plastic deformation along the cutting edge near the fracture site. Fractographic and longitudinal examinations were carried out at high-power magnification with SEM. Stereomicroscopy revealed 88 flexural cases and 12 torsional cases. Fractomicrographs verified 91 flexural cases with fatigue striations and three torsional cases with circular abrasion marks. Six instruments showed characteristics of both flexural and torsional failures. Cracks, microcracks, and pittings were common findings on longitudinal micrographs. Our study demonstrated that inspecting the fractured surface at high-power magnification by SEM is a better method to reveal the mode of NiTi rotary instrument separation.