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Background Genetic polymorphisms that affect the availability and secretion of dopamine can affect the risk of obesity. Objectives To investigate the relationship between pediatric obesity and cardiovascular risk factors (CRF) with the polymorphisms of “Fat Mass and Obesity Associated” (FTO) rs9939609, “Dopamine Receptor type 2” (DRD2) rs6277 and “Ankyrin Repeat and Kinase Domain Containing 1” (ANKK1) rs18000497 genes. Methods Case-Control study conducted with 226 pediatric patients from 5 to 16-years of age. The two main groups, Obese (O) and Eutrophic (E), were subdivided according to the value of HOMA-IR into obese with insulin resistance (ORI) or insulin sensitivity (OSI) and eutrophic resistant (ERI) or sensitive (ESI) to insulin. According to the presence of two or more CRF, they were subdivided into metabolically unhealthy or metabolically healthy groups: Obese Metabolically Unhealthy (OMU), Obese Metabolically Healthy (OMH), Eutrophic Metabolically Unhealthy (EMU) and Eutrophic Metabolically Healthy (EMH). Polymorphisms were determined by real-time Polymerase Chain Reaction (PCR) or Restriction Fragment Length Polymorphisms (PCR-RFLP). Results In the obese group, the higher the number of risk alleles of FTO and ANKK1 genes isolated and the three genes combined, the higher the mean BMI (p |