The aim of study was to investigate the differences between three-dimensional (3D) endosonography and two-dimensional (2D) endosonography in visualizing damage to the anal sphincter complex. 33 patients with a history of damage to the anal sphincters were examined with a 10 MHz rotating endoprobe. Cross-sectional images of the anal sphincters were stored on a 3D system during retraction of the endoprobe through the anal canal. Cross-sectional images (2D) were compared with reconstructed projections (3D) according to five parameters relating to damage of different parts of the sphincter muscles as well as scar-tissue formation in the rectovaginal septum. Depending on whether the investigator felt confident in diagnosis of scar tissue being present or not a numerical value of 1 or 0 was assigned. In this way a scale from 0 to 5 points was achieved, which ideally should be identical in 3D and 2D. Overall both observers felt diagnostic confidence in a median of five parameters (range 4-5) using 3D, compared with a median of four parameters (range 3-5) using 2D (p=0.001). When only assessing the four parameters relating to damage of different parts of the sphincter-muscles the observers felt diagnostic confidence in eight more cases using 3D than 2D. This difference did not reach statistical significance. The overall agreement between the two observers comparing all five parameters was 98.2% using 3D and 87.9% using 2D. 3D anal endosonography improves diagnostic confidence in detecting damage to the anal sphincter complex. The agreement between the two observers was acceptable using 2D but better when using 3D. The 3D method may improve the selection of patients for surgical repair of the anal sphincter complex.