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The present work aimed to analyze the mechanical behaviors of Ni-Ti endodontic instruments using FEM. Firstly, a program package was exploited preliminarily for the professional analysis of mechanical behaviors of endodontic instruments using ANSYS command stream, APDL (ANSYS Parametric Design Language) and UIDL (User Interface Design Language) languages. The parameterized characteristic variables include preliminarily the shape of the cross-section, number, taper, degree of helix. Secondly, we analyzed the torsional and bending behaviors of various endodontic instruments, including ProTaper, Hero 642, Mtwo, ProFile, Quantec, NiTiflex and W-type models. The impact of the shape of cross-sections, taper, tip diameter and the degree of helix on the torsional or bending behaviors of Ni-Ti endodontic instruments were studied. Our results showed that the stress was concentrated in the flute more or less for all the models. The cross-section had great impact on the mechanical properties of NiTi endodontic instruments. The factors required to regard include the cross-sectional inertia, depth of the flute, central area, radial land and peripheral surface ground. The taper was found to strongly correlate with the stress distribution along the shaft while the tip diameter had more influence on the maximum stress values under torsional moment. However, there was no obvious difference in torsional or bending stress intensity and distribution for models with different degrees of helix. Finally, we can conclude that it is possible to give some suggestions to the optimizing design and clinical usage of Ni-Ti endodontic instruments through the mechanical analysis.