SummaryBackgroundDyslipidemia is an important risk factor for the development of several diseases. The genetic component of hypertriglyceridemia has been studied in adults, but little is known in children.ObjectiveThe objective is to evaluate the association of two variants in APOA5 (rs662799) and APOA1 (rs5072) with triglyceride (TG) levels in Mexican children.MethodsAnthropometric parameters were measured in 1559 Mexican children 5–14 years of age. DNA was isolated from blood samples. Lipid profiles and glucose concentrations were determined from serum and genotyping of rs662799, and rs5072 was performed using TaqMan® technology. Additive and dominant models adjusted for age, gender and body mass index were used to evaluate the association of these single nucleotide polymorphisms with TG levels.ResultsChildren with high TG levels were found to have a higher body mass index and waist circumference as well as a worse lipids profile and glucose levels (p < 0.001). Additive and dominant models demonstrated a significant association between the rs662799 and rs5072 with TG. The dominant model showed the strongest significant association (OR = 1.81; 95% CI 1.46–2.24; p = 5.40 × 10⁻⁰⁸ for rs662799 and OR = 1.54; 95% CI 1.05–2.25; p = 2.60 × 10⁻⁰² for rs5072).ConclusionThe minor alleles of rs662799 (APOA5) and rs5072 (APOA1) modulate TG levels in Mexican children.