In recent years, a subgroup of individuals with obesity has been described as having a lower risk of metabolic and cardiovascular complications. These individuals have what is referred to as metabolically healthy obesity (MHO), which has a favorable metabolic profile and a lower probability of long-term complications. The definition of this subtype in children is not clear. The aim of the present study was to determine whether Homeostasis Model Assessment (HOMA) above a set threshold could be the marker of metabolically unhealthy obesity (MUO) in children, or a parameter that can be used in the overall assessment. It is intended to compare the International Diabetes Federation (IDF) criteria against HOMA in the diagnosis of MUO. This observational, retrospective, cohort study included children with obesity and analyzed their metabolic state by means of blood testing and dual-energy X-ray absorptiometry. A total of 96 patients were included, 44.8% boys and 55.2% girls, ages 6-17 years. The patients with MHO according to the HOMA criterion were younger (P = 0.001), had a lower body mass index (BMI) z score (P = 0.006), waist-height index (P = 0.009), hip-height index (P = 0.010), blood glucose (P = 0.003), insulin (P < 0.001), and lower percentages of total fat (P = 0.002), trunk fat (P = 0.001), and android fat (P = 0.009) than those with MUO. The logistic regression analysis according to IDF criteria detected an area under the receiver operating characteristic (ROC) curve of 0.659 (95% CI 0.546-0.771; P = 0.009) versus the area under the ROC curve of 0.854 (95% CI 0.777-0.931; P < 0.001) for the HOMA definition. Therefore, the determination of the metabolic state according to HOMA has greater sensitivity and specificity than the IDF criteria. The multivariate analysis in children classified according to HOMA revealed that the percentage of total fat and gynoid fat distributions and triglyceride level could be markers of a healthy or unhealthy metabolic state in children with obesity (P < 0.001). The use of HOMA as a single criterion was demonstrated to be an effective and simple detector of adiposity, which predicts the metabolically healthy obesity in children.