Background: Metabolic syndrome (MS) is closely linked to obesity; however, not all individuals with obesity will develop obesity-related complications and a metabolically healthy obesity (MHO) group is also described. Objective: To perform a multivariate analysis (MVA) of the anthropometric and biochemical data in pediatric patients with obesity to reveal a “phenotype” predictive for MS. Methods: We analyzed 528 children with obesity (OB) and 119 normal-weight pediatric patients (NW). Adiposity indices were recorded, and MS was detected. MVA was performed. Results: Analysis of the structure of correlation of the variables showed that the variables of waist circumference (WC), body mass index (BMI), and estimated fat mass (eFM) were positively correlated with each other as a whole. In addition, the variables of the triglycerides (TG), triglyceride–glucose (TyG) index, and visceral adiposity index were positively correlated with each other as a whole, although none were correlated with the variables of BMI z-score, waist-to-height ratio, WC, eFM, or weight. The variables that related to insulin resistance (IR) and dyslipidemia were crucial for the early stratification of patients at risk of MS. Conclusions: Independently of body weight, IR, dyslipidemia, hypertriglyceridemia, and fat distribution seem to be the strongest MS risk factors. The early detection of and intervention in these modifiable risk factors are useful to protect children’s health.