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Abstract Brain-derived neurotrophic factor (BDNF) has an important role in energy balance. It suppresses food intake, reduces hepatic glucose production and converts white fat into brown fat in adipose tissue, leading to energy dissipation, lowered blood glucose and a lean phenotype. Studies have shown that the single nucleotide polymorphism (SNP) Val66Met within BDNF may be associated with obesity, insulin sensitivity, type 2 diabetes mellitus (T2DM) and dyslipidemia. The objective of the study was to investigate the association of the Val66Met polymorphism with body mass index (BMI), fasting glucose levels and lipid profile in Serbian adolescents. The study included 308 randomly selected healthy adolescents, 153 (49.68%) boys and 155 girls (50.32%), 15 years of age. Data including age, gender, height, weight, lipid profile and fasting glucose were recorded. Genotyping was performed by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. No association of this polymorphism was found with BMI and lipid profile. However, significant association was observed between this polymorphism and fasting blood glucose (FBG). Carriers of a Val/Val genotype had significantly higher mean values of fasting glucose level compared to carriers of Val/ Met and Met/Met genotypes (p = 0.01). To confirm these results multiple linear regression analysis was performed. Body mass index and gender were taken as covariates. Carriers of the Val/Val genotype had significantly higher levels of FBG (β = -0.152, p = 0.02). A statistically significant association between BMI and glucose level was also observed (β = 0.124,p = 0.033). This polymorphism could be associated with fasting glucose level in Serbian adolescents, thus further research would be of great interest to validate these results.