The degree of 18-fluorodeoxyglucose (FDG) uptake is previously reported to correlate with physical examination and laboratory tests for evaluating disease activity in patients with rheumatoid arthritis. The clinical validity of F-18-FDG positron emission tomography (PET) has not been evaluated in juvenile idiopathic arthritis (JIA). To assess the relationship between F-18-FDG PET uptake and disease activity in children with JIA. A total of 560 joints in 28 children (mean age, 5.4 years; range, 1-16 years) with JIA who had undergone whole-body F-18-FDG PET before treatment were retrospectively assessed clinically, biochemically and radiographically. PET images were assessed independently by two readers. We investigated the relationships between the degree of synovial F-18-FDG uptake and radiographic and clinical symptoms and laboratory findings. Joint tenderness and swelling had a positive association with abnormal F-18-FDG uptake in the joint [odds ratio (OR) 5.37, 7.12, respectively]. The standardized uptake value (SUV) max correlated with the neutrophil count, plasma C-reactive protein (CRP), erythrocyte sedimentation rate (ESR) and matrix metalloproteinase (MMP) 3. Joint erosion (OR, 6.17), soft-tissue swelling (OR, 3.77), major joints involvement (OR, 3.50), tenderness (OR, 5.22), and CRP concentration in plasma (OR, 1.81) were positively associated with SUVmax. The degree of F-18-FDG uptake may be associated with the severity of synovitis in children with JIA.