Background Familial Mediterranean fever (FMF) is suggested to be associated with increased risk of atherosclerosis. Epicardial adipose tissue (EAT) thickness is used in prediction of atherosclerotic risk. The aim of our study was to evaluate EAT thickness in FMF patients for early detection of risk of atherosclerosis and to be compared with its level in healthy controls. Methods Thirty 6- to 18-year-old children with FMF and 30 age- and sex-matched children (control group) were included in the study. Disease characteristics, disease severity and Mediterranean fever gene mutations were recorded. EAT thicknesses was measured by echocardiography. Results EAT in patients’ group was significantly greater than that of controls (5.21 ± 2.3 vs. 2.81 ± 2.96 mm, p = 0.001) and was correlated with cholesterol level and platelets count (p = 0.047 and 0.018, respectively). Conclusion This study concluded that EAT thickness was statistically increased in FMF patients than controls with a positive correlation with cholesterol level and platelet count. This finding suggests a higher risk for atherosclerosis in these patients. Follow-up study is needed to verify the effect of treatment of FMF on the EAT thickness. Further studies with larger number of patients following-up EAT are needed to verify this finding.