Aim: The aim of the study was to determine the relationship between malocclusion and palatal rugae patterns and its reliability in gender determination of adolescents aged 13–18 years. Materials and methods: A total of 90 children with 30 in each of skeletal class I, II and III groups respectively were included in the study. The lateral cephalograms of the study samples were analyzed cephalometrically using ANB angle, WITS appraisal and beta angle and categorized as skeletal class I, class II or class III sagittal skeletal jaw relation. Sassouni's Archial analysis was used to reconfirm skeletal jaw relation and also to assess treatment needs. Palatal rugae of each sample were recorded to study the patterns. Thomas and Kotze classification was followed for rugae pattern analysis. Results: No definite rugae print pattern could be associated with any particular sagittal skeletal jaw relation in the present study. Female population of class II skeletal malocclusion showed a significant difference for number of rugae on the right and left sides of mid palatine raphe. Discriminant function analysis showed no significance when the number of rugae were compared among males and females for gender determination. Conclusion: As rugoscopy was neither found to provide absolute conclusive evidence in identification of any particular jaw relationship nor gender determination, combination with more reliable forensic methods would help in better personal identification. Clinical significance: Palatal rugae and craniofacial skeleton develop at the same embryonic period. Developmental factors that cause malocclusions should also reflect in the palatal rugae patterns. There exists a deficiency in studies in samples of younger age group and hence the need of the study.