Introduction/Objective The objective of this study is to use scanning electron microscopy (SEM) to analyze working surfaces of new manual and rotary endodontic instruments and to check possible existence of manufacture dirt particles or defects on the working surface. Methods In this study, we used three sets of new manual instruments: K-File, KF (Dentsply Maillefer, Switzerland) and Hedstorm Files, HF (SybronEndo Co, USA) and three sets of mechanical Ni-Ti instruments-type K3 (SybronEndo Co, USA) and BioRaCe (FKG DENTAIRE Swiss Dental Products, Switzerland). The instruments were analyzed using SEM method at 170 × magnification while semi-quantitative energy dispersive x-ray analysis was used to determine chemical composition of dirt particles. Fisher test (p < 0.05) was applied in statistical analysis. Results Results showed that none of the instruments were defect-free. The most common defect type was the presence of metal strips, which were noticed at the surface of all tested instruments. Debris was present on all manual and only one type of mechanical instruments, K3 (39% in the apical and 33% in the middle third). Fretting was noticed in all manual KF and all mechanical instruments of the K3 group. Pitting was common in all manual instruments, KF (33% in the apical and 39% in the middle third) and HF (11% in the apical and 6% in the middle third). Corrosion of the working surface, metal flash, and disruption of the cutting edge were marked only in the KF group. Conclusion Manufacture defects were noticed in all instruments and the most common type of irregularity were metal strips. Electropolished surface of BioRaCe instruments showed no debris of organic origin.