Individual variations in the fat mass and obesity-associated (FTO) gene have been associated with obesity and BMI in diverse populations, but there are no reports in young Mexicans. We explored the association of a common FTO single-nucleotide polymorphism (SNP, rs805704) with obesity-related phenotypes in Mexican young adults. The FTO-SNP was genotyped using the fluorescent polarization method in college-age, apparently healthy subjects from the “UP AMIGOS” cohort (n = 251, 18 - 25 yrs). Homozygotes for the A allele (15%, n = 38) were heavier (1.6 kg/m2 and6.2 kg) and had a larger waist circumference (WC,4.8 cm) than G allele carriers. The FTO genotype was associated with BMI, weight and WC independently of age and sex and explained 2.7 to 3.1% of the variance in obesity-related phenotypes. The FTO genotype was also associated with fasting glucose (P = 0.0283). No other associations were found in the additive model. Despite our small sample size, we found that the FTO-rs805704 genotype influences obesity-related phenotypes young Mexicans. Previously observed FTO associations with fasting glucose were replicated. Previously reported associations with other metabolic traits likely represent the long-term consequences of obesity.