Statement of the Problem: Palatal rugae have been considered equivalent to fingerprints, as they are unique to each individual. It has been shown that palatal rugae are associated with specific racial groups and are known to aid sex identification. Due to the lack of any published data on palatal rugae morphology on Iranian children, the present study was performed.Purpose: The present study aimed to investigate differences in the morphology of individual palatal in a sample of Iranian children. Additionally, it is intended to develop discriminant function to identify sex, based on rugae morphology.Materials and Method: A total of 120 pre-orthodontic casts were evaluated for different rugae patterns using the Thomas and Kotze classification. The casts were equally distributed between sexes with an age range of 6-12 years. Rugae length, shape, and associated morphology were recorded and the independent t test and Chi-square test were used to compare the mean and relationship between the attributes. The discriminant function analysis was applied to the data in order to determine the applicability of palatal rugae patterns as an aid for sex identification.Results: While the total rugae count showed an insignificant difference between the males and females, the rugae count on the right side of the palates showed a significant difference (p= 0.046). The primary rugae were most common in both sexes, followed by the secondary and fragmentary rugae. The most prevalent rugae shape between both sexes was the wavy rugae followed by the curve and straight shapes in males and the straight and curve shapes in females. A significant difference was observed in the number of the curve rugae between the sexes. Discriminant function analysis allowed sex differentiation with an accuracy of 60.8%.Conclusion: Palatal rugae shapes are unique to each individual and could be used as a potential tool for sex identification. Further research on a larger sample is required to fully confirm the application of this method (e.g. in forensic medicine) as a complementary technique for sex identification.