Obesity and its related emotional and physical consequences are a worldwide problem. Obese individuals are usually stigmatized. This study is proposed to assess the correlation between body mass index, gender and age with psychiatric symptoms among Iranian students. A number of 9172 students aged 10-18 years (53.5% girls and 46.5% boys) from all provinces of Iran participated in this study. Data was collected using the global school based health survey questionnaire of the World Health Organization (GSHS-WHO). Overall, prevalence of predictors of having emotional problems, depression and anxiety were 27.8%, 29.7% and 11.5% respectively. Girls had significantly higher prevalence of predictors of psychiatric symptoms. Overall obesity was a protective factor against emotional problems OR (CI95%):0.79(0.65-0.98), but it was attributable to obese boys OR (CI95%):0.72(0.55-0.95). Depression and anxiety symptoms were higher in intermediate school girls and high school girls and boys. More attention should be paid to girls' psychological problems. Besides, obesity had an indirect relation with predictors of having psychiatric problems in Iranian boys and it might be due to: (1) parents' beliefs about heaviness as a predictor of healthiness, (2) boys' lower vulnerability to psychological consequences of obesity and (3) lower pressure from parents on their obese sons to lose weight.