Objective: To analyze, using confocal microscope, the three-dimensional characteristics of the root-end cavity preparations completed in root apices of extracted teeth determining their area, perimeter, circularity and cavo-surface angle. Study design: Thirty-two single-rooted extracted teeth underwent endodontic treatment and apical resection. Root-end cavities were prepared according to 4 protocols, as follows: Group1, stainless steel ultrasonic tips (SST) at 33 KHz power; Group 2, SST at 30 KHz power; Group 3, diamond-coated ultrasonic tips (DCT) at 30 KHz power; and Group 4, DCT at 33 KHz power. Finally, root-end cavity was evaluated using a confocal microscope, recording its area, perimeter, circularity and cavo-surface angle. Results: The largest cavity perimeter was found in the Group 2 (4.8 ± 1.6 mm) (p > 0.05). Root-end cavities performed using SST showed larger areas than those performed with DCT (p = 0.03). The power of vibration or the tip type did not show correlation with the perimeter, circularity and cavo-surface angle of the root-end cavity (p > 0.05). Conclusions: Confocal microscopy is a useful approach to study the three-dimensional characteristics of the root- end cavity