This ApoA5-1131C allele of rs662799 variant is related with a higher serum triglyceride levels, and it contributes to increase risk of cardiovascular disease. The aim of the present investigation was to evaluate single nucleotide polymorphism rs662799 in APOA5 gene and its associations with cardiovascular risk factors, MS, and serum adipokine levels. The study involved a population of 1,002 Caucasian obese subjects. Measurements of body weight, waist circumference, fat mass, arterial blood pressure, blood glucose, C-reactive protein, insulin levels, insulin resistance (HOMA-IR), lipid profile, and adipokines levels were recorded. Genotype of ApoA5 gene polymorphism (rs662799) and prevalence of metabolic syndrome (MS) were evaluated. The distribution of the rs662799 polymorphism in this adult population (n = 1,002) was 88.3% (n = 885) (TT), 11.4% (n = 114) (TC), and 0.3% (n = 3) (CC). No significant differences were found between the 2 genotypes in the anthropometric data, MS, or blood pressure. Triglyceride levels were higher in C-allele carriers (delta total group: 19.7 ± 2.1 mg/dL: p = 0.02) than non C-allele carriers. HDL-cholesterol levels were lower in C-allele carriers (delta total group: -6.7 ± 1.1 mg/dL: p = 0.02) than non C-allele carriers. Adiponectin levels were lower in C-allele carriers (delta total group: -11.6 ± 1.0 mg/dL: p = 0.02) too. In C-allele carriers, logistic regression analysis showed an increased risk of hypertriglyceridemia (odds ratio OR = 2.1, 95% confidence interval CI = 1.2-3.4, p = 0.001) and percentage of low-HDL-C (OR = 2.2, 95% CI = 1.3-3.7, p = 0.002) after adjusting by body mass index and age. C-allele carriers of rs662799 of APOA5 gene showed high rates of low levels of HDL and hypertriglyceridemia, with differences in triglyceride, HDL cholesterol, and adiponectin levels in Caucasian obese subjects.