The aim of this population-based study was to estimate the prevalence of overweight and obesity in public and private schools of Santos city, Brazil. We evaluated a total of 10,822 children aged 7 to 10 years old. Determination of overweight and obesity was obtained by the 85th and 95th percentiles of BMI for age, respectively, as proposed by CDC in 2000. The overall prevalence rates of overweight and obesity were 15.7% (CI 95%= 15.0% to 16.4%) and 18.0% (17.3% to 18.7%), respectively. The prevalence of overweight was 13.7% (12.6% a 14.8%) in boys and 14.8% (13.7% a 15.9%) in girls of public schools. In private schools, the rates were 17.7% (15.7% to 19.7%) in boys and 22.2% (20.0% to 24.4%) in girls. Obesity was found in 16.9% (15.7% to 18.1%) of the boys and 14.3% (13.2% to 15.4%) of the girls of public schools. In the private schools, 29.8% (27.4% to 32.2%) of the boys and 20.3% (18.2% to 22.4%) of the girls were obese. We concluded that the prevalence of obesity in public and private schools in the city of Santos is higher than other studies conducted in Brazil and in other countries of Latin America. Private schools showed higher prevalence rates of obesity than public schools (p= 0.001).