Obesity is a disease that is affected by environmental conditions as well as genetic predisposition. This is a case-control study that aimed to investigate the relationship between FTO rs9939609 polymorphism and obesity. The relation between the rs9939609 polymorphism and obesity in 80 ower-weight (BMI≥30) and 131 under/normal weight (BMI<30) subjects was examined. The allele and genotype frequencies of each group were determined by the allele counting method. The relationship between single nucleotide exchange and obesity risk was calculated using the odds ratio. Statistical analyzes were performed with SPSS 18.0. Results: The frequency of T allele was 0.58 and 0.45 respectively in the healthy and overweight group when allele frequencies of both groups were compared. The change in allele frequency increased the obesity rate by 1.8 fold. The rs99399609 polymorphism increases obesity risk by2.7 fold in the homozygotes model. Conclusions: In this research, we found statistically significant results in allele frequency difference and allele positivity. The relationship between rs9939609 polymorphism and obesity will be highlighted by larger population studies.