Case-control studies evaluating the factors associated with childhood obesity are scarce in Brazil. We aimed to analyze the factors associated with obesity in Brazilian schoolchildren enrolled in the School Health Program.A case-control study was conducted on 80 schoolchildren aged 7 to 9 years, 40 of them obese and 40 of normal weight according to the cut-off points established by the World Health Organization (2007). Weight, height and waist circumference were obtained. Socioeconomic, demographic, health, eating behavior and lifestyle data were collected by applying a questionnaire to the person responsible and by determining his/her nutritional status. A binary unconditional logistic regression model (univariate and multivariate) was used for data analysis. The prevalence of obesity was 7.21%. The final model showed that duration of breast-feeding .6 months of age (OR 5.3; 95% CI: 1.3-22.1), excess weight of the person responsible (OR 7.1; 95% CI: 1.2-40.2), a sedentary level of physical activity (OR 4.1; 95% CI: 1.1-15.5), and fast chewing (OR 7.4; 95% CI: 2.1-26.9) were significantly associated with childhood obesity. The factors associated with obesity in schoolchildren were duration of breast-feeding .6 months, persons responsible with excess weight, and sedentary children who chew fast. The present study contributes information to be used for the health actions planned by the School Health Program.