© 2018 The Author(s). Background: Up to 80% of children with juvenile idiopathic arthritis (JIA) develop arthritis involving their temporomandibular joint (TMJ). Recent studies have questioned the sensitivity of an abnormal MRI in the diagnosis of active arthritis. Methods: 122 children without arthritis undergoing contrast MRI of the head were prospectively consented to undergo a simultaneous contrast MRI of their TMJs. As a comparison point, the initial MRI of the TMJ of 35 newly diagnosed children with JIA were retrospectively scored. The presence and size of effusion and contrast enhancement were measured in the left TMJ in all subjects. Results: 62/122 (51%) controls compared to only 10/35 JIA (29%) patients had an effusion (p = 0.022). Contrast enhancement was present in ≥97% of both groups, although the size of the enhancement was, on average, 0.2 mm larger in controls (1.1 ± 0.24 vs 0.88 ± 0.27 mm, p < 0.001). Among JIA patients, the size of the enhancement correlated inversely with disease duration (r = - 0.475, p = 0.005). Chronic changes were present in none of the controls versus 2/35 (5.5%) of the JIA patients (p = 0.049). Conclusion: Findings consistent with minimally active TMJ arthritis appear to be equally likely in children with JIA as compared to non-inflamed controls, while this and other studies confirm that chronic changes are specific to JIA. Thus, small amounts of effusion or contrast enhancement, in the absence of chronic changes, should be interpreted with caution.