Objective To compare serum amyloid A concentrations between overweight and eutrophic children and adolescents and to relate it to lipid profiles, glucose tolerance, and carotid intima-media thickness. Methods One hundred children and adolescents (mean age: 10.8±3.16 years) were included and divided into two groups: overweight and non-overweight. The following were evaluated: Z-score body mass index, carotid intima-media thickness, lipid metabolism biomarkers (lipid profile and apolipoproteins A1 and B), inflammatory biomarkers (ultra-sensitive C-reactive protein and serum amyloid A), and glucose homeostasis model assessment of insulin resistance. Results The groups were homogeneous in age, sex, and pubertal stage. Higher levels of triglycerides, apolipoprotein B, homeostasis model assessment of insulin resistance, ultrasensitive C-reactive protein, serum amyloid A, and carotid intima-media thickness were observed in the overweight group. In the multivariate analysis, age (OR=1.73; 95%CI: 1.16-2.60, p=0.007), Z-score body mass index (OR=3.76; 95%CI: 1.64-8.59, p=0.002), apolipoprotein-B (OR=1.1; 95%CI: 1.01-1.2, p=0.030), and carotid intima-media thickness (OR=5.00; 95%CI: 1.38-18.04, p=0.014) were independently associated with serum amyloid A levels above the fourth quartile of the studied sample (>9.4mg/dL). Conclusion Overweight children and adolescents had higher serum amyloid A concentrations than eutrophic children. There was an independent association between higher concentrations of serum amyloid A and Z-score, body mass index, apolipoprotein B, and carotid intima-media thickness, indicating the importance of this inflammatory biomarker in identifying the early risk of atherosclerosis.