The aim of the study was to assess the presence and characteristics of subclinical synovitis using power Doppler (PD) ultrasonography on patients with juvenile idiopathic arthritis (JIA) in clinical remission and compare the findings with those of healthy children. A cross-sectional study was carried out involving the clinical (physical exam, functional capacity and laboratory tests) and ultrasonography evaluation of 34 joints (synovial fluid/hypertrophy, PD signal and bone erosion). Subclinical synovitis was defined as the presence of synovial hypertrophy/joint effusion with or without any PD signal. Thirty-six patients (11.5 ± 3.74 years) and 36 controls (sex and age matched) were evaluated (2,448 joints). Twenty-seven patients were in remission on medication (mean duration: 1.8 ± 2.2 years). Subclinical synovitis was detected in 41.7% patients and 11.1% controls (p = 0.003). Erosion was detected in three patients (8.3%). Subclinical synovitis was found in 38/1,224 (3.1%) joints in the patients (most affected: radiocarpal wrist, anterior elbow and tibiotalar ankle) and 8/1,224 (0.6%) joints in the controls (most affected: radiocarpal wrist). Differences in subclinical synovitis between patients and controls were found in the elbows (p = 0.033) and ankles (p = 0.006). A greater frequency of subclinical synovitis was found in patients with the extended oligoarticular or polyarticular subtypes (p = 0.013), those at an older age at disease onset (p = 0.007) and using methotrexate (p = 0.049). Patients with JIA in remission exhibit subclinical synovitis more frequently than controls. Subclinical synovitis was more frequent in patients with the polyarticular involvement and those at an older age at disease onset.