Background: The measurement of subepicardial adipose tissue thickness (SATT) has been found to be related to insulin resistance (IR) in adults. Until now, the association between SATT and IR has not been evaluated in obese prepubertal children. We aimed to determine the relation of SATT with clinical anthropometric and metabolic parameters and to provide cutoff value of SATT associated with IR in obese prepubertal children. Methods: Fifty-two obese (mean age: 9.5 +/- 1.6 years, 29 female) and 31 lean prepubertal age- and gender-matched subjects (mean age: 9.2 +/- 1.4 years, 12 female) were evaluated by echocardiography. SATT was measured by transthoracic echocardiography. Results: SATT (6.54 +/- 1.38 mm) and homeostatic model assessment-insulin resistance (HOMA-IR) (3.2 +/- 2) values of obese prepubertal subjects were significantly higher than those of the lean subjects (3.72 +/- 0.57 mm and 1.6 +/- 1) in the control group (both p < 0.001). Bivariate correlation analysis showed significant correlation between SATT, age, body mass index (BMI), waist circumference (WC), hip circumference (HC), waist-to-hip ratio (WHR), mid-arm circumference (MAC), triceps skin fold (TSF) thickness, insulin, and HOMA-IR (r = 0.547, r = 0.524, r = 0.543, r = 0.431, r = 0.289, r = 0.402, r = 0.400, r = 0.328, r = 0.289, p < 0.05, respectively). As an optimal cutoff point, an SATT of 4.33 mm determined IR with 93.3% sensitivity and 51% specificity. Conclusions: Our study on obese prepubertal children showed that SATT was significantly correlated with age, BMI, WC, HC, MAC, TSF, insulin, and HOMA-IR.