Behçet's disease (BD) is a systemic vasculitis affecting all sizes of arteries and veins. Approximately 5-10% of patients with BD are present during childhood. The chronic nature of the disease may lead to serious cardiovascular complications over time including early atherosclerosis. Increased levels of epicardial adipose tissue (EAT) and carotid intima-media thickness (CIMT) are considered early signs of subclinical atherosclerosis. Ongoing chronic inflammation may cause to increase in both EAT and CIMT. In this study, we aimed to evaluate CIMT and EAT in children with BD and determine their relationship with the clinical manifestations and course of the disease. This cross-sectional study evaluated 30 patients with juvenile-onset BD and age-sex-matched 20 healthy controls. The CIMT and EAT thickness were measured by the same paediatric cardiologist. The association between clinical features, baseline disease activity, disease duration, EAT thickness and CIMT was also evaluated. Thirty children with BD and 20 age-sex-matched healthy volunteers enrolled in the study. The most common BD-related feature was oral aphthous (n=30), followed by mucocutaneous findings (n=22). Uveitis was observed in 5 patients, vascular involvement in 4, neurological involvement in 4, and gastrointestinal involvement in 2. All patients were inactive at the time of evaluation. The EAT thickness was significantly higher in patients while CIMT levels revealed no significant differences. However, there was no correlation between disease duration, baseline disease activity, and EAT thickness. Increased EAT thickness may be a risk factor for early atherosclerosis in patients with BD. The EAT thickness was found to be significantly higher in paediatric BD patients. Confirmation of results in larger series may provide better insight into early screening for risk factors in these patients.