Background: Consideration of mandibular third molar is important from orthodontic perspective due to several factors such as, lower anterior arch crowding, relapse in lower anterior region, interference with uprighting of mandibular first and second molars during anchorage preparation and molar distalization. The aims of this study were to assess of gender differences in the mandibular third molar position and compare and evaluate whether there is any differences in the results provided by CT scan and lateral reconstructed radiograph. Materials and Methods: The sample of present study consisted of 39 patients (18 males and 21 females) with age range 11-15 years. CT images for patients who were attending at Al Suwayra General Hospital/the Computerized Tomography department. Computed tomographic images were obtained for The distance from Xi point to distal surface of permanent mandibular second molar was measured in both three dimensional volumetric images and two dimensional CT derived lateral image. The statistical analyses included: means, standard deviations. Paired t-test was used to compare between the two methods and independent t-test was used in verifying the genders difference. Results: The results showed that there was high significant method difference between 3D CT and 2D image and gender differences was observed in values of linear measurements of present study, as males showed higher mean values than females. Conclusion: There is high accuracy of measurement on CT images, so CT scan is advisable during the diagnosis and treatment plan of orthodontic cases.