Background and Aims: The NPY gene has 4 exons, and it is located at 7p15.1. The main genetic variant described in this gene is rs16147. The aim of this study was to investigate the relationship of NPY rs16147 with body weight, insulin resistance, serum adipokine levels, and risk of metabolic syndrome (MetS). Methods: A population of 1,005 obese patients was analyzed in a cross-sectional survey. Weight, fat mass, waist circumference, blood pressure, basal glucose, C-reactive protein, insulin, insulin resistance (homeostasis model assessment of insulin resistance [HOMA-IR]), lipid profile, and adipocytokine (leptin, adiponectin, and resistin) levels were measured. The genotype of the NPY gene polymorphism (rs16147) was studied. Results: Body mass index (1.0 ± 0.1; p < 0.05), weight (2.8 ± 0.4 kg; p < 0.05), fat mass (1.8 ± 0.3 kg; p < 0.05), waist circumference (1.9 ± 0.2 cm; p < 0.05), leptin level (15.4 ± 8.2 ng/mL; p < 0.05), insulin level (5.1 ± 1.3 mIU/L; p < 0.05), and HOMA-IR (1.4 ± 0.1 units; p < 0.05) were lower in A allele carriers than in non-A allele carriers in males. Males with an A allele had a lower percentage of MetS (54.8 vs. 69.1%; p < 0.05), central obesity (94.5 vs. 100%; p < 0.05), and hyperglycemia (24.7 vs. 33.8%; p < 0.05) than non-A allele carriers. Logistic regression analysis indicated that male non-A allele carriers had an increased risk of MetS (odds ratio [OR] = 1.26, 95% confidence interval [CI] = 1.17-1.83; p = 0.034), an increased risk of central obesity (OR = 1.08, 95% CI = 1.02-1.11; p = 0.044), and an increased risk of hyperglycemia (OR = 1.20, 95% CI = 1.09-1.79; p = 0.028) after adjusting for age. Conclusions: In obese males, the rs164147 polymorphism of the NPY gene is associated with leptin, insulin level, HOMA-IR, and an increased risk of MetS and its related phenotypes, such as central obesity and hyperglycemia.