Background Macro-nutrients can influence on body weight through their interactions with FTO gene polymorphisms. This study aimed to investigate the association between FTO gene rs9939609 polymorphism with macro-nutrients intake.Methods This cross-sectional study was carried out on 196 overweight adults. The rs9939609 SNP in FTO was genotyped. Dietary intake was assessed by a valid 168-item semi-quantitative food frequency questionnaire (FFQ). The association between dietary macro-nutrients and the FTO genotype were assessed using linear regression after adjustments for sex, age, physical activity, triglycerides, fasting blood sugar (FBS), and low density lipoprotein (LDL).Results The higher carbohydrates (p=0.000), fat intake (p=0.009) and calorie intake (p=0.001) were significantly associated with FTO gene risk allele (P=0.001). Carriers of the AA/AG genotype of rs9939609 had significantly higher calorie, fat, and carbohydrate intake than the carriers of the TT genotype (p=0.019, p=0.010, & p=0.000, respectively).Conclusion The dietary carbohydrate and fat intake were associated with FTO genotype. Further studies are warranted to investigation of these interactions and the underlying mechanisms.