Background The present study aims to estimate childhood overweight and obesity prevalence and their association with individual and population-level correlates in Eastern and Western European countries. Methods Data were obtained from the School Children Mental Health in Europe, a cross-sectional survey conducted in 2010 in Italy, Germany, the Netherlands, Romania, Bulgaria, Lithuania and Turkey. The sample consists of 5,206 school children aged 6 to 11 years old. Information on socio-demographics, children’s height and weight, life-style and parental attitude were reported by the mothers. Country-level indicators were obtained through several data banks. Overweight and obesity in children were calculated according to the international age and gender-specific child Body Mass Index cut-off points. Multivariable logistic regression models included socio-demographic, lifestyle, mothers’ attitude, and country-level indicators to examine the correlates of overweight. Results Overall prevalence was 15.6% (95% CI = 19.3-21.7%) for overweight and 4.9% (95% CI = 4.3-5.6%) for obesity. In overweight (including obesity), Romanian children had the highest prevalence (31.4%, 95% CI = 28.1-34.6%) and Italian the lowest (10.4%, 95% CI = 8.1-12.6%). Models in the pooled sample showed that being younger (aOR = 0.93, 95% = CI 0.87-0.97), male (aOR = 1.24, 95% CI = 1.07-1.43), an only child (aOR = 1.40, 95% CI = 1.07-1.84), spending more hours per week watching TV (aOR = 1.01, 95% CI =1.002-1.03), and living in an Eastern Country were associated with greater risk of childhood overweight (including obesity). The same predictors were significantly associated with childhood overweight in the model conducted in the Eastern region, but not in the West. Higher Gross Domestic Product and Real Domestic Product, greater number of motor and passenger vehicles, higher percentage of energy available from fat, and more public sector expenditure on health were also associated with lower risk for childhood overweight after adjusting for covariables in the pooled sample and in the east of Europe, but not in the West. Conclusions Prevalence rates of overweight and obesity in school children is still high, especially in Eastern regions, with some socio-demographic factors and life-styles associated with being overweight. It is also in the Eastern region itself where better macro-economic indicators are related with lower rates of childhood overweight. This represents a public health concern that deserves special attention in those countries undertaking economic and political transitions.