OBJECTIVE: 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). PATIENTS AND METHODS: 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. RESULTS: 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. CONCLUSIONS: 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.