Many new rotary files systems have been introduced, however, limited research has been conducted related to the surface irregularities of these files and if these have any effects on the files themselves. Hence, the aim of the present study was to analyze surface irregularities of the ProTaper® Universal rotary files (PTU) and the ProTaper Next? rotary files (PTN) before and after instrumentation in curved canals. The main objective was to investigate the nature of these irregularities and how they might influence the use and fracture of rotary files during root-canal treatments. The files were examined pre-operatively using a stereomicroscope and scanning electron microscopy(SEM) to analyze surface imperfections and the presence of particles. Mesial roots of forty extracted mandibular molars were selected. Each instrument was used to prepare one of the mesial canals. The files were then rinsed with alcohol, and autoclaved and analyzed again. Of the 80 files used in this study, five files fractured, five files unwound and seven files were curved or bent and they all belonged to the PTU group. Irregularities and debris could be visualized with the SEM on both unused PTU and PTN files. Most of the debris was found associated with deeper milling grooves and defects on the surface of the metal. Surface analysis of the files that were used and sterilized were performed and the SEM images demonstrated organic debris, metal flash, and crack formation and initiation of fractures for both file types. All files showed machining grooves, metal flash, debris, and defects on cutting edges. These irregularities appear to be critical in the accumulation of debris and initiation of fatigue and crack propagation within the NiTi alloy. The accumulation of debris could be a concern due to the potential exchange of organic debris between patients.