Abstract Background Abdominal obesity plays a major role in development of metabolic syndrome. Computed tomography and dual-energy X-ray absorptiometry were used to assess abdominal fat in children but carry risk of radiation and are expensive. Assessing abdominal fat using ultrasound in obese children could be a reasonable alternative with evaluating its relationship to obesity indicators especially insulin resistance. Methods We conducted a cross sectional study on 46 obese children and adolescents aged between 6-16 years to evaluate abdominal adiposity by using ultrasound. Subcutaneous fat thickness (SFT) and visceral fat thickness (VFT) were measured and correlated to anthropometric measures, fasting lipid profile, HOMA-IR and liver function tests. Results VFT was strongly correlated with the BMI (r = 0.397, p=0.006) and HOMA- IR (r = 0.413, P = 0.004) with AUC for VFT as a predictor of insulin resistance of 0.858 and cut of point of > 2.98 cm . VFT also correlated positively with serum triglycerides (r = 0.421, p=0.004) and serum ALT (r = 0.370, P=0.011). VFT correlated negatively with HDL (r= -0.313, P= 0.034 ). Conclusions Ultrasound could be a useful tool for measuring abdominal fat thickness in children and adolescents. Ultrasound measured VFT could be an appropriate prognostic factor for insulin resistance, hypertriglyceridemia, and elevated liver enzymes.