Objective To determine the frequency of radiographic changes in the temporomandibular joint, in a representative population of patients with Juvenile Idiopathic Arthritis (JIA) and to compare with findings in healthy controls matched by sex and age. Patients and Methods One hundred and thirty-seven panoramic radiographies (PR) from JIA patients of a pediatric rheumatology outpatient clinic were prospectively evaluated and compared to 137 PR from healthy individuals. Results 102 (74.5%) JIA patients and 47 (34.3%) controls showed at least one radiological alteration (p < 0.001). The following radiographic alterations were more frequently observed in JIA patients than in controls: erosion (p < 0.001), altered condylar morphology (p < 0.001), disproportion between condylar process and the coronoid process (p < 0.001) and accentuated curve in the antegonial notch (p = 0.002). Twenty patients (14.6%) presented the four radiographic alterations simultaneously compared to only two controls (1.5%) (p < 0.001). Conclusion Due to the difference in the frequency of findings in the PR of patients and controls, we concluded that PR has value as a screening tool. In the presence of major changes in the mandible head in the PR of patients with a confirmed diagnosis of JIA, MRI should be considered to detect an active inflammatory process in this joint.