MRI is used for the detection of synovitis in juvenile idiopathic arthritis (JIA). We developed a whole-body MRI protocol, consisting of coronal, post-contrast mDixon images, which is fast and offers good coverage of peripheral joints and spine. A prospective study including 32 adolescent and young adult patients with JIA revealed that 43.8% of patients had synovitis in at least one joint on imaging that was not detectable clinically. The proportion of patients with subclinical synovitis was similar in clinically active and inactive patients. This could lead to identification of unsuspected inflammation in JIA patients with potential impact on their treatment.