Aim: To assess morphological alterations of ProTaper rotary NiTi files before and after continuous use by scanning electron microscopy (SEM). Study Design: 30 root canals were chosen with an angle between 15 and 30º. Before starting to prepare the canals the files were observed microscopically using a scanning electronic microscope. The ProTaper sequence recommended by the manufacturer was used, with NaOCl as irrigant. The instruments were sterilised after every three canals were shaped. The instruments were observed with the same microscope after shaping each canal, until 30 root canals were shaped. The criteria used for checking the instruments were: blunt cutting edges, disruption of cutting edge, microfractures, fatigue cracks, metal flash, dentine remains. Results: Many microscopic defects were found such as: cutting edge breaks (up to 70%); fatigue cracks, between 33 and 100%. No microfractures were found. An S1 and an SX file were fractured. Conclusion: ProTaper instruments are quite reliable if used following usual requirements.