Deviation of the major apical foramen from the anatomical root apex is a recognized phenomenon. To determine the frequency, position and mean distance of the major apical foramen from the anatomical root apex, 230 roots of permanent teeth were examined stereomicroscopically and radiographically. Radiographic analysis was used to establish how accurate the conventional radiograph was in displaying such a deviation. The frequency of deviation of the major foramen, determined stereomicroscopically, was 76%, and depended on the type of teeth examined. Radiographic analysis of the same sample revealed 57% of root canals had asymmetry of the root canal foramen. Agreement of stereomicroscopic and radiographic findings was found to be 61%. The most frequent deviation of the major foramen was on the distal root surface (29%), but this was not statistically significant. The mean distance between the deviation of the major foramen and the anatomical root apex was 0.99 mm. The study indicates that the clinician should consider deviation of the foramen during root canal treatment, as the deviation could not easily be detected radiographically.