Leptin plays an important role in satiety signaling and is related to obesity. Variants of leptin gene (LEP) have been associated to differences in plasma leptin levels and obesity-related phenotypes. The purpose of this study was to evaluate the association of LEP 3'HVR and leptin concentrations and obesity-related traits in our population. Anthropometrics and systolic/diastolic pressure were measured in 210 unrelated Brazilian individuals. Blood samples were collected for quantification of leptin, glucose and lipids and DNA extraction. LEP 3'HVR polymorphic region was amplified by PCR and fragments were analyzed by polyacrylamide gel electrophoresis. Obesity was associated with hypertension, hyperglycemia, obesity-related traits, plasma leptin and serum lipids (p < 0.05). The frequency of LEP 3'HVR class I alleles (I/I + I/II genotypes) was higher in obese (p = 0.043) than in non-obese individuals. Multivariate logistic regression showed that the risk for obesity is nine times higher in hypertensive individuals and two times higher in class I alleles carriers. The presence of class I alleles was associated with increased BMI and WC. Plasma leptin was related to class I alleles in women (p < 0.05). No association was found between LEP 3'HVR and hypertension or risk factors for CAD in our sample. Our results suggest that LEP 3'HVR is an important predictor for obesity-related traits and leptin plasma levels.