Introduction: The purpose of this study is to use Cone-Beam Computed Tomographic images to compare the skeletal and dental changes with MSE (Maxillary skeletal expander) and Hyrax appliance. Material and Method: 15 patients in MSE group and 8 patients in Hyrax group who met inclusion criteria were included. We used Independent-T test to compare the angulation of palatal sutures, bone bending and molar tipping between two groups. Result: In MSE group, the angulation of palatal sutures was 0.62 degree while it was 7.50 degree in the Hyrax group. (P< 0.01) The bone bending was 1.39 degrees in MSE group and it was 3.77 degrees in Hyrax group. (P<0.01) Molar angulation changes were 4.05 degrees in MSE group and 10.05 degrees in Hyrax group. (P<0.01). Estimated molar tipping in MSE group was 2.66 degrees and 6.28 degrees in Hyrax group. Conclusion: This study showed that the MSE appliance was able to produce a more parallel palatal suture opening, less bone bending and less molar tipping than the Hyrax appliance. Cone-Beam Computed Tomography is a useful tool in quantifying the skeletal and dental changes after palatal expansion.