The APOA5-1131C allele is related to a worse lipid profile and metabolic response to diet interventions. The present study was designed to investigate the effect of SNP rs662799 on the lipid profile of patients with obesity after a hypocaloric diet with a Mediterranean pattern enriched in ω-6 polyunsaturated fatty acids (PUFA). A population of 362 Caucasian patients with obesity was evaluated. Anthropometric evaluation and serum parameters (lipid profile, insulin, homeostasis model assessment (HOMA-IR), glucose, C reactive protein, and adipokines) were measured at basal time and after 12 weeks. All subjects were genotyped rs662799. The APOA5 variant distribution among the 362 patients with obesity was the following: 87.2% (n=316) (TT) were homozygous for the T allele, 12.2% (n=44) (TC) were heterozygous, and 0.6% (n=2) (CC) were homozygous for the C allele. There were only significant differences in triglyceride levels between genotype groups. After 12 weeks of intervention, the following parameters improved in both genotype groups: adiposity parameters, systolic blood pressure, total cholesterol, LDL cholesterol, leptin, adiponectin, and ratio leptin/adiponectin. Insulin levels (delta: -3.5±0.2 UI/L vs. -1.2±0.6 UI/L; p=0.03), HOMA-IR (delta: -1.6±0.1 units vs. -0.3±0.2 units; p=0.01) and triglyceride levels (delta: -18.8±4.1 mg/dl vs. -3.7 ±3.0 mg/dl; p=0.02) decreased in non-C allele carriers. Our data demonstrate that the minor C allele of the APOA5 gene (rs662799) produces a worse response in triglyceride levels, insulin levels, and HOMA-IR after a ω-6 PUFA enriched hypocaloric diet with Mediterranean pattern.