-Obesity is considered a disease with multiple etiologies. Recent advances in technology have pointed candidate genes that are related to weight gain in several populations. However, in countries with ethnic miscegenation, such as Brazil, studies of this nature with students are still scarce. The aim of the present study was to compare anthropometric variables of Brazilian male students according to the genotypes of the rs9939609 of the FTO gene. In order to do so, 205 participants underwent body mass, height, waist circumference and skinfold thickness measurements. Body mass index (BMI), waist-to-height ratio and body fat percentage were calculated. Volunteers were characterized as overweight according to the BMI-for-age z-score. Participants were genotyped according to the single nucleotide polymorphism rs9939609 of the FTO gene (AA, AT and TT). ANOVA one-way with Bonferroni's post hoc was performed to compare genotypes and anthropometric variables. Odds Ratio was calculated to reveal increased chances of presenting higher body mass index z-score, waist-to-height ratio and body fat percentage. Participants homozygous for the A allele presented significantly higher values of BMI-for-age z-score (0.38±1.01 vs. -0.29±1.15), waist circumference (77.15±6.51 vs. 72.85±7.36 cm) and waist-to-height ratio (0.44±0.04 vs. 0.42±0.04) when compared to individuals with the TT genotype. The A allele of the rs9939609 of the FTO gene seems to influence in the adiposity of male students. (0,38±1,01 vs. -0,29±1,15), circunferência da cintura (77,15±6,51 vs. 72,85±7,36 cm) e relação cintura-estatura (0,44±0,04 vs. 0,42±0,04)