The aim of this study was to evaluate the influence of the flexion angle of files on the decentralization of root canals during instrumentation. Fifteen lower incisors were instrumented with Protaper Universal files and radiographed in two directions (mesiodistal and buccolingual) before and after instrumentation with a #15 K-file in position for evaluating the flexion angle of files. The specimens were also scanned before and after instrumentation using micro-computed tomography to obtain the canal area and the distance from the center position of the file to the canal walls. Sections located 1.0 mm (end of the canal), 3.0 mm (apical third), 9.0 mm (middle third), and 15.0 mm (cervical third) from the apex were verified. After instrumentation, the flexion angles of files decreased by an average of 0.76º in the buccolingual direction and 1.92º in the mesiodistal direction (p < 0.001); the canal area increased by an average of 0.58, 0.37, 0.23 and 0.13 mm2 from the cervical to the end of the root canal (p < 0.001). Non-instrumented areas were observed on the buccal and lingual walls, and effective action of files was determined on the mesial and distal walls. The sections from the end of the canal showed canal deviation toward the lingual wall, whereas the other sections showed deviation toward the buccal wall. The flexion angles of files influence the final shape of the root canal, resulting in file decentralization along the pathway of the canal.