This investigation aimed to develop a radiographic 3D cephalometric index to grade severity of dentofacial deformity in patients with juvenile idiopathic arthritis (JIA), and to perform a validation against expert evaluations. Data were collected from a population-based Nordic JIA cohort of 240 patients that received a cone-beam computed tomography (CBCT) scan approximately 17 years after onset of JIA. The cohort was randomized into two groups: A baseline group for establishing the index (n = 210) and a test group (n = 30). The standardized index generation process led to the inclusion of six radiographic outcome measures, each representing different facets of dentofacial deformities. Specific severity scores were established for three domains; dentofacial asymmetry (0-8), vertical deviation (0-8), and sagittal deviation (0-8). An overall dentofacial deformity index score was computed by aggregating the scores from the six variables, with the total score ranging from 0 to 24. The validity of the index was assessed by comparing the index score with expert evaluations. Based on the generated index, 10 patients exhibited severe deformities. Reliable agreement between data-generated index scores and expert assessments was found. A 3D radiographic dentofacial deformity index was generated and tested. This index can support an objective assessment of the severity of dentofacial deformities related to JIA in a clinical setting and future research.