This study aimed to measure serum levels of the proinflammatory protein S100A12, investigate clinical as well as contrast enhanced magnetic resonance imaging findings of temporomandibular joint inflammation among juvenile idiopathic arthritis patients and to find out the correlation between each of them, moreover with different disease parameters as temporomandibular joint inflammation may occur without clinical manifestations; it is in need for thorough evaluation and S100A12 may be a future anti-inflammatory treatment in JIA. Twenty patients with Juvenile Idiopathic Arthritis (JIA) and 10 healthy control subjects underwent measurement of S100A12 serum concentrations by sandwich ELISA. Temporomandibular Joints (TMJs); clinical and post contrast Magnetic Resonance Imaging (MRI) examinations were performed. MRI findings were scored. Results showed that TMJ arthritis was detected in 80% of JIA patients using MRI. Serum S100A12 levels were significantly increased in patients compared to controls. Serum concentrations of S100A12 and total MRI scores were significantly higher in JIA patients with active disease compared to those without activity. Systemic and polyarticular JIA patients showed significant increase in S100A12 levels and total MRI scores compared to those with oligoarticular JIA. The MRI TMJ abnormalities revealed significant association with clinical signs of TMJ inflammation but not with symptoms. A significant correlation was found between serum S100A12 concentrations and MRI score as well as between each of them and different clinical, laboratory disease parameters. Serum S100A12 levels showed significant positive correlation with synovial enhancement score. To conclude TMJ arthritis could be detected in most cases of JIA patients using contrast enhanced MRI. Increased S100A12 levels may point to synovial inflammation. Clinical signs of TMJ arthritis may be used as filter for MRI examination. Further studies on larger scale of JIA patients are needed for monitoring TMJ inflammation and S100A12 may be a potential target of future anti-inflammatory therapy.