Background Because of the individuality of the palatal rugae, they are applicable for human identification purposes the same as the fingerprints. Therefore, it is important to assess the effect of different factors on rugae characteristics. We assessed the characteristic changes of the palatal rugae following extraction and expansion during orthodontic treatments. Before and after orthodontic treatment dental casts of 30 patients were scanned by 3Shape Trios 3D intraoral scanner, and superimposed in Geomagic X 2018 software. Displacement of 13 reference points was analyzed in three dimensions. The length of the palatal rugae was also measured. SPSS version 22.0 was applied for data analysis, using independent t test, sample t test, and chi-square test. Results The alterations in the mean palatal rugae length were significant in the first right and third right ridges after extraction, and right and left second ridges after expansion treatment (P < 0.05). Changes in coordinates in the X, Y, and Z axes were significant at 8 points on the rugae after extraction, and 5 points after expansion treatment (P < 0.05). The changes in the sum of means of displacements were significant at all 13 points after extraction and expansion treatments (P < 0.05). Conclusions The palatal rugae do not remain stable during expansion and extraction orthodontic treatments. Some changes occurred in length, and the most medial and most lateral points on each ridge were displaced. The length of the incisive papilla did not change during treatment; thus, it can serve as a stable landmark. If we consider palatal rugae as an individual landmark, we can refer the patients after orthodontic treatment for scanning of their palatal rugae to document their post treatment pattern; but it should be noted that treatment relapse may change it again.

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