Background: Juvenile Idiopathic Arthritis (JIA) is a chronic disease that affects 0.6 - 1.9 /1,000 children. Persistent joint inflammation conditions cartilage damage and erosions. Recent studies have shown that clinical examination significantly underestimates joint inflammation, with ultrasound having a higher sensitivity. The aim of this study was determined the prevalence of subclinical synovitis by musculoskeletal ultrasound in Mexican children with JIA in remission. Methods: Cross-sectional study, patients with JIA in clinical remission based on the Wallace criteria were included, with and without pharmacological treatment, we also included a control group of healthy children. The evaluation was performed by a certified Rheumatologist in Pediatric Musculoskeletal Ultrasound by EULAR. Joints clinically examined were also evaluated following the standard guidelines. Results: A total of 37 JIA patients with clinical remission and 33 healthy children were evaluated (1260 joints scanned), subclinical activity was detected in 15/37 (40.5%) patients and none of healthy children; 14 patients were still on treatment (93.3%). The subclinical activity was detected by gray scale in 22/1260 (1.7%) or by power Doppler (PD) in 15/1260 (1.1%) joints, the knee was involved in 13/22 (59%) joints. The subtype mainly affected was the rheumatoid factor-positive (FR) polyarticular (33.3%), erosions were detected in three patients (8%). In the knee, we observed slight distention of the supra patellar recess, evidenced in 19/33 healthy children (57.5%), predominantly among children aged 4 to 8 years. When comparing the groups with or without subclinical synovitis, no statistically significant differences were found with regard to age, evolution time or acute phase reactants. Conclusions: Subclinical synovitis was detected in 40.5% of the patients in clinical remission using gray scale or by power Doppler, mainly on those who were still on treatment. The most affected subtype was the rheumatoid factor-positive polyarticular, the knees were the most frequent involved. In the healthy children, a slight distention of the supra patellar recess was observed in almost half of cases.