The aim of this study was to determine the contribution of individual and school characteristics to the variability in body mass index (BMI) z-scores of 7 to 10 years old children. Anthropometric and sociodemographic data from two cross-sectional studies conducted with schoolchildren from the 2nd to the 5th grades of elementary schools were analyses (n = 2,936 in 2002, and n = 1,232 in 2007). Multilevel modeling was used to estimate variations in BMI at child and school levels. The contribution of the school context to the overall variability of BMI z-score was small but significant in 2002 (3.3%-4.4%) and in 2007 (2.4%-5.3%), showing that schoolchildren from private schools had a higher BMI compared to those from public schools. The monthly family income showed, in general, a negative association with BMI z-score in 2002 and a positive association in 2007, for both sexes. The consumption of sweets showed a negative effect in the BMIs of children. In both surveys, overweight/obese mothers and excessive birth weight were positively associated with BMI z-score. Mother's weight status had a higher influence on the overall variability of BMI in both surveys. In conclusion, school and child characteristics contributed to the variance in children's weight status. The results imply that overweight/obesity childhood prevention programs should focus on strategies of family engagement to be more effective.