Body mass index (BMI), usually used as a body fatness marker, does not accurately discriminate between amounts of lean and fat mass, crucial factors in determining metabolic syndrome (MS) risk. We assessed the predictive ability of the estimate of FM (eFM) calculated using the following formula: FM = weight − exp(0.3073 × height2 − 10.0155 ×d-growth-standards/standards/body-mass-index-for-age-bmi-for-age weight− 1 + 0.004571 × weight − 0.9180 × ln(age) + 0.6488 × age0.5 + 0.04723×male + 2.8055) (exp = exponential function, score 1 if child was of black (BA), south Asian (SA), other Asian (AO), or other (other) ethnic origin and score 0 if not, ln = natural logarithmic transformation, male = 1, female = 0), to detect MS in 185 prepubertal obese children compared to other adiposity parameters. The eFM, BMI, waist circumference (WC), body shape index (ABSI), tri-ponderal mass index, and conicity index (C-Index) were calculated. Patients were classified as having MS if they met ≥ 3/5 of the following criteria: WC ≥ 95th percentile; triglycerides ≥ 95th percentile; HDL-cholesterol ≤ 5th percentile; blood pressure ≥ 95th percentile; fasting blood glucose ≥ 100 mg/dL; and/or HOMA-IR ≥ 97.5th percentile. MS occurred in 18.9% of obese subjects (p < 0.001), with a higher prevalence in females vs. males (p = 0.005). The eFM was correlated with BMI, WC, ABSI, and Con-I (p < 0.001). Higher eFM values were present in the MS vs. non-MS group (p < 0.001); the eFM was higher in patients with hypertension and insulin resistance (p < 0.01). The eFM shows a good predictive ability for MS. Additional to BMI, the identification of new parameters determinable with simple anthropometric measures and with a good ability for the early detection of MS, such as the eFM, may be useful in clinical practice, particularly when instrumentation to estimate the body composition is not available.