The aims of this study were to evaluate palatal rugae patterns using three-dimensional (3D) digital models; to compare relevant digital model conversion techniques for identification;to develop a protocol for overlay registration;to determine changes in palatal rugae individual patterns through time and following orthodontic treatment;and to investigate the efficiency and accuracy of 3D matching processes between different individuals.Five cross sections in the anteroposterior dimension and four cross sections in the transverse dimension were used to compute eighteen 2D variables.Thirteen 3D variables were defined.The results demonstrated that 2D images were not sufficient for comparing different digital model conversion techniques.The 3D landmarks showed no statistically mean differences over time and as a result of orthodontic treatment.No statistically mean difference was found between the three different conversion techniques, when using twelve 3D palatal landmarks for comparison.Certain landmarks showed more significant impact on the matching process and were arranged by strength and importance.A 3D approach was developed and utilized for human verification and identification.