Aim of the study: was to evaluate three dimensionally the skeletal and dental effects of headgear in growing patients using cone beam C.T.Material and Methods: 24 growing female patients with Class II Division 1 malocclusion with age range from 8 to 12 years were divided into 2 groups, 12 treatment who received headgear for 6 months and 12 controls who received no treatment for 6 months. Measurements on cone beam C.T scans were done using the Anatomage software (Anatomage, San José, California, USA) to evaluate the possible skeletal and dental effects of headgear treatment. Statistical analysis for parametric data was done using paired t-test, was used to study the changes after treatment within each group. For non-parametric data, Wilcoxon signed-rank test was used to study the changes after treatment within each group.Changes after treatment were studied Mann-Whitney U test was used to compare between the two groups. This test is the non-parametric alternative to Student's t-test and Inter-observer reliability (agreement) was measured using Cronbach’s alpha reliability coefficient. Results showed a significant distal molar movement with a mean of 2.23mm± 1.6mm for the right maxillary first molar and 2.5±1.6 for the left molar. All other skeletal and dental measurements have shown non-significant change except UR6MD/PP and UL1/PP. The reliability of the software measurements were considered acceptable for both superimposition and 3D analysis.Conclusion: The headgear was an effective tool for molar distalization. Nevertheless, there will always remain the issue of compliance. Adequate distal movement of the molars could be achieved in 6 months, without significant extrusion or buccal rolling. No significant skeletal maxillary and mandibular changes were noted. This was attributed to the short treatment period of 6 months which was not sufficient to produce skeletal effect. Cone beam CT and Anatomage software were efficient and reliable tools in the diagnosis and measurement of skeletal and dental changes.