The purpose of this study was to compare the stress distributions of NiTi rotary instruments based on their cross-sectional geometries of triangular shape-based cross-sectional design, S-shaped cross-sectional design and modified rectangular shape-based one using 3D FE models. NiTi rotary files of S-shaped and modified rectangular design of cross-section such as Mtwo or NRT showed larger stress change while file rotation during simulated shaping. The stress of files with rectangular cross-section design such as Mtwo, NRT was distributed as an intermittent pattern along the long axis of file. On the other hand, the stress of files with triangular cross-section design was distributed continuously. When the residual stresses which could increase the risk of file fatigue fracture were analyzed after their withdrawal, the NRT and Mtwo model also presented higher residual stresses. From this result, it can be inferred that S-shaped and modified rectangular shape-based files were more susceptible to file fracture than the files having triangular shape-based one.