We examined the joint and independent associations between VAT and LF with insulin sensitivity (IS) and lipids in seventy-one obese adolescents (BMI ≥ 95th, 14.9 ± 1.8 years). VAT was assessed by magnetic resonance imaging, and LF was quantified by proton magnetic resonance spectroscopy. IS was evaluated by a 3 -h hyperinsulinemic (80 mU·m(-2)·min(-1)) euglycemic clamp. Independent associations between VAT and LF on metabolic variables were assessed in mutually adjusted multivariate models. The joint association between VAT and LF on metabolic variables was assessed by categorizing participants into a low VAT + low LF group (n = 35), high VAT + low LF group (n = 26), or high VAT + high LF group (n = 10), based on a VAT median split (1.17 kg) and high (≥5%) and low (<5%) LF. Both VAT and LF were independently associated with fasting insulin, 2 h insulin, insulin AUC, IS, and triglycerides (P < 0.05). Adolescents with high VAT + high LF had higher 2 h glucose, glucose AUC, 2 h insulin, triglycerides, and lower insulin sensitivity compared to adolescents with high VAT only (P < 0.025 for all). In obese adolescents, VAT and LF were independently associated with insulin sensitivity and dyslipidemia, and the concomitant presence of VAT and LF is strongly associated with metabolic risk factors.