Objective: The objectives of this study were to determine the thickness of skull bones, namely frontal, parietal, and occipital bones in Class I, Class II, and Class III patients. Materials and Methods: Three hundred subjects who reported to the Department of Orthodontics requiring orthodontic treatment within the age group 17-35 were selected for the study. They were subdivided into three groups of 100 each according to the skeletal and dental relation. Profile radiographs were taken and the tracings were then scanned, and uploaded to the MATLAB 7.6.0 (R 2008a) software. The total surface areas of the individual bones were estimated by the software, which represented the thickness of each bone. Result: Frontal bone was the thickest in Class III malocclusion group and the thinnest in Class II malocclusion group. But the parietal and occipital bone thickness were not significant. During gender differentiation in Class I, malocclusion group frontal bone thickness was more in males than females, In Class II, malocclusion parietal bone thickness was more in males than females. No statistically significant difference exists between genders, in Class III malocclusion group. During inter-comparison, the frontal bone thickness was significant when compared with Class I and Class II malocclusion groups and Class II and Class III malocclusion groups. Conclusion: The differences in skull thickness in various malocclusions can be used as an adjunct in diagnosis and treatment planning for orthodontic patients. It was found that the new method (MATLAB 7.6.0 [R 2008a] software) of measuring skull thickness was easier, faster, precise, and accurate.