The purpose of this study was to evaluate the morphological structure of palatal rugae in Turkish orthodontic subjects with different sagittal skeletal malocclusions. Orthodontic dental casts of 105 patients (Class I [23 females, 12 males]; 35, Class II [18 females, 17 males]; and 35, Class III [14 females, 21 males] 10–22 years old) were analyzed for rugae patterns. Palatal rugae pattern and number, direction of rugae alignment, shape of incisive papilla were analyzed. Modified Thomas and Kotze classification was performed to analyze palatal rugae characteristics. The data were analyzed using the Kruskal–Wallis test. Wavy and curved types were the most common types of rugae pattern in all groups (Class I, Class II, Class III). As regards to the number of primary and secondary rugae on the left and right sides, there was no statistically significant difference among subjects with different skeletal malocclusions. Droplet-shaped incisive papilla was the most common form of incisive papillae among different skeletal malocclusion groups. The most common palatal rugae were direction type arranged in the horizontal direction. All rugae patterns were unique for each individual. The use of antemortem or postmortem palatal rugae records may facilitate identification of the suspects in forensic investigations by enabling facial reconstruction through skeletal malocclusions.